ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. It is commonly used in genomics research and is also a very important data source included in MyVariant.info.
myvariant.py is an easy-to-use Python wrapper to access MyVariant.Info services. By utilizing myvariant.py, you can easily access ClinVar data with only a few lines of code.
In this demo, we will show you how to use myvariant.py to query for ClinVar data by a few use cases.
Install myvariant.py is easy, as pip is your friend:
pip install myvariant
You can find more usage examples from MyVariant.py PyPI page. The detailed API documentation can be found at http://myvariant-py.readthedocs.org .
Now you just need to import it and instantiate MyVariantInfo class:
import myvariant
mv = myvariant.MyVariantInfo()
myvariant.py allows you to query for annotation information of a given variant or variants by calling getvariant or getvariants method. You can also customize the output by passing specific field name or names as parameters. For more information about field names available in MyVariant.info, please check the detailed documentation.
mv.getvariant('chr17:g.7578532A>G', fields = 'clinvar')
{u'_id': u'chr17:g.7578532A>G',
u'_version': 1,
u'clinvar': {u'allele_id': 27396,
u'alt': u'G',
u'chrom': u'17',
u'cytogenic': u'17p13.1',
u'gene': {u'id': u'7157', u'symbol': u'TP53'},
u'hg19': {u'end': 7578532, u'start': 7578532},
u'hg38': {u'end': 7675214, u'start': 7675214},
u'hgvs': {u'coding': [u'LRG_321t8:c.281T>C',
u'LRG_321t5:c.2T>C',
u'LRG_321t6:c.2T>C',
u'LRG_321t7:c.2T>C',
u'LRG_321t1:c.398T>C',
u'LRG_321t2:c.398T>C',
u'LRG_321t3:c.398T>C',
u'LRG_321t4:c.398T>C',
u'NM_001276697.1:c.-80T>C',
u'NM_001126118.1:c.281T>C',
u'NM_001126115.1:c.2T>C',
u'NM_001126116.1:c.2T>C',
u'NM_001126117.1:c.2T>C',
u'NM_000546.5:c.398T>C',
u'NM_001126112.2:c.398T>C',
u'NM_001126113.2:c.398T>C',
u'NM_001126114.2:c.398T>C'],
u'genomic': [u'LRG_321:g.17337T>C',
u'NG_017013.2:g.17337T>C',
u'NC_000017.11:g.7675214A>G',
u'NC_000017.10:g.7578532A>G']},
u'omim': u'191170.0011',
u'rcv': {u'accession': u'RCV000013151',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'age_of_onset': u'All ages',
u'identifiers': {u'medgen': u'C1835398',
u'omim': u'151623',
u'orphanet': u'524'},
u'name': u'Li-Fraumeni syndrome 1 (LFS1)'},
u'last_evaluated': u'1999-01-01',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_000546.5(TP53):c.398T>C (p.Met133Thr)',
u'review_status': u'no assertion criteria provided'},
u'ref': u'A',
u'rsid': u'rs28934873',
u'type': u'single nucleotide variant',
u'variant_id': 12357}}
mv.getvariant('chr17:g.7578532A>G', fields = 'clinvar.variant_id')
{u'_id': u'chr17:g.7578532A>G',
u'_version': 1,
u'clinvar': {u'variant_id': 12357}}
out = mv.getvariant('chr17:g.7578532A>G', fields = ['clinvar.variant_id','clinvar.rcv.accession'])
In this case, your output is clinvar *variant id* and *rcv accession number* of the variant.out
{u'_id': u'chr17:g.7578532A>G',
u'_version': 1,
u'clinvar': {u'rcv': {u'accession': u'RCV000013151'}, u'variant_id': 12357}}
out = mv.getvariant('chr6:g.26093141G>A', fields = ['clinvar.rcv.accession', 'exac.af', 'dbnsfp.sift.converted_rankscore'])
Here, you get the *rcv accession number* from ClinVar, *allele frequency* information from EXAC and *sift converted_rankscore* from dbnsfp for your target variant as the output.out
{u'_id': u'chr6:g.26093141G>A',
u'_version': 1,
u'clinvar': {u'rcv': [{u'accession': u'RCV000000019'},
{u'accession': u'RCV000000020'},
{u'accession': u'RCV000000021'},
{u'accession': u'RCV000000022'},
{u'accession': u'RCV000000023'},
{u'accession': u'RCV000000024'},
{u'accession': u'RCV000000025'},
{u'accession': u'RCV000117222'},
{u'accession': u'RCV000178096'}]},
u'dbnsfp': {u'sift': {u'converted_rankscore': 0.91219}},
u'exac': {u'af': 0.032}}
out = mv.getvariants(['chr6:g.26093141G>A', 'chr11:g.118896012A>G'], fields = 'clinvar.gene.symbol')
querying 1-2...done.
Here, your output is the *gene symbol* of both variants.out
[{u'_id': u'chr6:g.26093141G>A',
u'_score': 1.0,
u'clinvar': {u'gene': {u'symbol': u'HFE'}},
u'query': u'chr6:g.26093141G>A'},
{u'_id': u'chr11:g.118896012A>G',
u'_score': 1.0,
u'clinvar': {u'gene': {u'symbol': u'SLC37A4'}},
u'query': u'chr11:g.118896012A>G'}]
myvariant.py also allows you to query for a specific field or fields in MyVariant.info.
mv.query('clinvar.rcv.accession:RCV000013151')
{u'hits': [{u'_id': u'chr17:g.7578532A>G',
u'_score': 16.53367,
u'cadd': {u'_license': u'http://goo.gl/bkpNhq',
u'alt': u'G',
u'anc': u'A',
u'annotype': u'CodingTranscript',
u'bstatistic': 473,
u'chmm': {u'bivflnk': 0.0,
u'enh': 0.008,
u'enhbiv': 0.0,
u'het': 0.0,
u'quies': 0.008,
u'reprpc': 0.0,
u'reprpcwk': 0.0,
u'tssa': 0.0,
u'tssaflnk': 0.0,
u'tssbiv': 0.0,
u'tx': 0.819,
u'txflnk': 0.0,
u'txwk': 0.11,
u'znfrpts': 0.055},
u'chrom': 17,
u'consdetail': u'missense',
u'consequence': u'NON_SYNONYMOUS',
u'consscore': 7,
u'cpg': 0.07,
u'dna': {u'helt': 0.01, u'mgw': 0.24, u'prot': 4.04, u'roll': 1.29},
u'encode': {u'exp': 1100.13,
u'h3k27ac': 6.2,
u'h3k4me1': 16.04,
u'h3k4me3': 3.08,
u'nucleo': 1.8},
u'exon': u'5/11',
u'fitcons': 0.726386,
u'gc': 0.58,
u'gene': {u'ccds_id': u'CCDS11118.1',
u'cds': {u'cdna_pos': 588,
u'cds_pos': 398,
u'rel_cdna_pos': 0.23,
u'rel_cds_pos': 0.34},
u'feature_id': u'ENST00000269305',
u'gene_id': u'ENSG00000141510',
u'genename': u'TP53',
u'prot': {u'domain': u'ndomain', u'protpos': 133, u'rel_prot_pos': 0.34}},
u'gerp': {u'n': 5.48, u'rs': 367.5, u'rs_pval': 1.53237e-26, u's': 5.48},
u'grantham': 81,
u'isderived': u'TRUE',
u'isknownvariant': u'FALSE',
u'istv': u'FALSE',
u'length': 0,
u'mapability': {u'20bp': 1, u'35bp': 1},
u'min_dist_tse': 16,
u'min_dist_tss': 95,
u'mutindex': 34,
u'naa': u'T',
u'oaa': u'M',
u'phast_cons': {u'mammalian': 0.998,
u'primate': 0.809,
u'vertebrate': 1.0},
u'phred': 23.5,
u'phylop': {u'mammalian': 2.204, u'primate': 0.53, u'vertebrate': 4.641},
u'polyphen': {u'cat': u'benign', u'val': 0.237},
u'pos': 7578532,
u'rawscore': 3.913993,
u'ref': u'A',
u'segway': u'TF2',
u'sift': {u'cat': u'deleterious', u'val': 0},
u'type': u'SNV'},
u'clinvar': {u'allele_id': 27396,
u'alt': u'G',
u'chrom': u'17',
u'cytogenic': u'17p13.1',
u'gene': {u'id': u'7157', u'symbol': u'TP53'},
u'hg19': {u'end': 7578532, u'start': 7578532},
u'hg38': {u'end': 7675214, u'start': 7675214},
u'hgvs': {u'coding': [u'LRG_321t8:c.281T>C',
u'LRG_321t5:c.2T>C',
u'LRG_321t6:c.2T>C',
u'LRG_321t7:c.2T>C',
u'LRG_321t1:c.398T>C',
u'LRG_321t2:c.398T>C',
u'LRG_321t3:c.398T>C',
u'LRG_321t4:c.398T>C',
u'NM_001276697.1:c.-80T>C',
u'NM_001126118.1:c.281T>C',
u'NM_001126115.1:c.2T>C',
u'NM_001126116.1:c.2T>C',
u'NM_001126117.1:c.2T>C',
u'NM_000546.5:c.398T>C',
u'NM_001126112.2:c.398T>C',
u'NM_001126113.2:c.398T>C',
u'NM_001126114.2:c.398T>C'],
u'genomic': [u'LRG_321:g.17337T>C',
u'NG_017013.2:g.17337T>C',
u'NC_000017.11:g.7675214A>G',
u'NC_000017.10:g.7578532A>G']},
u'omim': u'191170.0011',
u'rcv': {u'accession': u'RCV000013151',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'age_of_onset': u'All ages',
u'identifiers': {u'medgen': u'C1835398',
u'omim': u'151623',
u'orphanet': u'524'},
u'name': u'Li-Fraumeni syndrome 1 (LFS1)'},
u'last_evaluated': u'1999-01-01',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_000546.5(TP53):c.398T>C (p.Met133Thr)',
u'review_status': u'no assertion criteria provided'},
u'ref': u'A',
u'rsid': u'rs28934873',
u'type': u'single nucleotide variant',
u'variant_id': 12357},
u'cosmic': {u'alt': u'C',
u'chrom': u'17',
u'cosmic_id': u'COSM43723',
u'hg19': {u'end': 7578532, u'start': 7578532},
u'mut_freq': 0.03,
u'mut_nt': u'T>C',
u'ref': u'T',
u'tumor_site': u'stomach'},
u'dbnsfp': {u'aa': {u'alt': u'T',
u'codonpos': 2,
u'pos': [u'133',
u'133',
u'1',
u'1',
u'1',
u'94',
u'133',
u'94',
u'133',
u'133',
u'133',
u'94',
u'94',
u'133',
u'94',
u'122',
u'1',
u'40',
u'133',
u'126'],
u'ref': u'M',
u'refcodon': u'ATG'},
u'alt': u'G',
u'ancestral_allele': u'A',
u'cds_strand': u'-',
u'chrom': u'17',
u'clinvar': {u'clinsig': 5,
u'rs': u'rs28934873',
u'trait': u'Li-Fraumeni_syndrome_1'},
u'ensembl': {u'geneid': u'ENSG00000141510',
u'proteinid': [u'ENSP00000410739',
u'ENSP00000352610',
u'ENSP00000484409',
u'ENSP00000478499',
u'ENSP00000481179',
u'ENSP00000478219',
u'ENSP00000269305',
u'ENSP00000481638',
u'ENSP00000482258',
u'ENSP00000398846',
u'ENSP00000391127',
u'ENSP00000482222',
u'ENSP00000480868',
u'ENSP00000391478',
u'ENSP00000482537',
u'ENSP00000482903',
u'ENSP00000425104',
u'ENSP00000423862',
u'ENSP00000424104',
u'ENSP00000473895'],
u'transcriptid': [u'ENST00000413465',
u'ENST00000359597',
u'ENST00000504290',
u'ENST00000510385',
u'ENST00000504937',
u'ENST00000610292',
u'ENST00000269305',
u'ENST00000620739',
u'ENST00000617185',
u'ENST00000455263',
u'ENST00000420246',
u'ENST00000622645',
u'ENST00000610538',
u'ENST00000445888',
u'ENST00000619485',
u'ENST00000615910',
u'ENST00000509690',
u'ENST00000514944',
u'ENST00000508793',
u'ENST00000604348']},
u'fathmm': {u'pred': [u'D',
u'D',
u'.',
u'.',
u'.',
u'.',
u'D',
u'.',
u'.',
u'D',
u'D',
u'.',
u'.',
u'D',
u'.',
u'.',
u'D',
u'D',
u'D',
u'.'],
u'rankscore': 0.99768,
u'score': [-6.7,
-6.7,
None,
None,
None,
None,
-6.7,
None,
None,
-6.7,
-6.7,
None,
None,
-6.7,
None,
None,
-6.7,
-6.7,
-6.7,
None]},
u'fathmm-mkl': {u'coding_group': u'AEFDGBHI',
u'coding_pred': u'D',
u'coding_rankscore': 0.99134,
u'coding_score': 0.99744},
u'genename': u'TP53',
u'gerp++': {u'nr': 5.48, u'rs': 5.48, u'rs_rankscore': 0.80555},
u'gm12878': {u'confidence_value': 0,
u'fitcons_rankscore': 0.74317,
u'fitcons_score': 0.702456},
u'h1-hesc': {u'confidence_value': 0,
u'fitcons_rankscore': 0.64003,
u'fitcons_score': 0.697927},
u'hg18': {u'end': 7519257, u'start': 7519257},
u'hg19': {u'end': 7578532, u'start': 7578532},
u'hg38': {u'end': 7675214, u'start': 7675214},
u'huvec': {u'confidence_value': 0,
u'fitcons_rankscore': 0.98419,
u'fitcons_score': 0.735409},
u'integrated': {u'confidence_value': 0,
u'fitcons_rankscore': 0.85317,
u'fitcons_score': 0.722319},
u'interpro_domain': [u'p53, DNA-binding domain',
u'p53-like transcription factor, DNA-binding',
u'p53/RUNT-type transcription factor, DNA-binding domain'],
u'lrt': {u'converted_rankscore': 0.55863,
u'omega': 0.072317,
u'pred': u'D',
u'score': 3.6e-05},
u'metalr': {u'pred': u'D', u'rankscore': 0.99123, u'score': 0.972},
u'metasvm': {u'pred': u'D', u'rankscore': 0.99543, u'score': 1.0972},
u'mutationassessor': {u'pred': u'N', u'rankscore': 0.08161, u'score': 0},
u'mutationtaster': {u'AAE': u'M133T',
u'converted_rankscore': 0.38995,
u'model': u'simple_aae',
u'pred': u'A',
u'score': 0.973129},
u'phastcons': {u'20way': {u'mammalian': 0.996,
u'mammalian_rankscore': 0.62353},
u'7way': {u'vertebrate': 0.989, u'vertebrate_rankscore': 0.5315}},
u'phylo': {u'p20way': {u'mammalian': 1.199,
u'mammalian_rankscore': 0.95998},
u'p7way': {u'vertebrate': 1.062, u'vertebrate_rankscore': 0.92612}},
u'polyphen2': {u'hdiv': {u'pred': [u'P',
u'B',
u'B',
u'B',
u'B',
u'B',
u'P'],
u'rankscore': 0.39305,
u'score': [0.551, 0.002, 0.004, 0.044, 0.001, 0.003, 0.674]},
u'hvar': {u'pred': [u'P', u'B', u'B', u'P', u'B', u'B', u'P'],
u'rankscore': 0.59325,
u'score': [0.804, 0.11, 0.062, 0.684, 0.113, 0.176, 0.858]}},
u'provean': {u'pred': [u'D',
u'D',
u'.',
u'.',
u'.',
u'.',
u'D',
u'.',
u'.',
u'D',
u'D',
u'.',
u'.',
u'D',
u'.',
u'.',
u'D',
u'D',
u'D',
u'.'],
u'rankscore': 0.62478,
u'score': [-2.93,
-2.92,
None,
None,
None,
None,
-3.01,
None,
None,
-2.92,
-2.92,
None,
None,
-3.01,
None,
None,
-2.76,
-2.92,
-2.96,
None]},
u'ref': u'A',
u'reliability_index': 9,
u'rsid': u'rs28934873',
u'sift': {u'converted_rankscore': 0.91219,
u'pred': [u'D',
u'D',
u'.',
u'.',
u'.',
u'.',
u'D',
u'.',
u'.',
u'D',
u'D',
u'.',
u'.',
u'D',
u'.',
u'.',
u'D',
u'D',
u'D',
u'.'],
u'score': [0.0,
0.0,
None,
None,
None,
None,
0.0,
None,
None,
0.0,
0.0,
None,
None,
0.0,
None,
None,
0.0,
0.0,
0.001,
None]},
u'siphy_29way': {u'logodds': 13.8301,
u'logodds_rankscore': 0.62644,
u'pi': {u'a': 1.0, u'c': 0.0, u'g': 0.0, u't': 0.0}},
u'uniprot': [{u'acc': u'B4E095', u'pos': u'94'},
{u'acc': u'P04637-2', u'pos': u'133'},
{u'acc': u'P04637-3', u'pos': u'133'},
{u'acc': u'E9PFT5', u'pos': u'40'},
{u'acc': u'P04637', u'pos': u'133'},
{u'acc': u'Q1MSW8', u'pos': u'133'},
{u'acc': u'E7EQX7', u'pos': u'133'}]},
u'dbsnp': {u'allele_origin': u'germline',
u'alleles': [{u'allele': u'A'}, {u'allele': u'G'}],
u'alt': u'G',
u'chrom': u'17',
u'class': u'SNV',
u'dbsnp_build': 133,
u'flags': [u'ASP',
u'LSD',
u'NSM',
u'PM',
u'PMC',
u'REF',
u'RV',
u'S3D',
u'U5'],
u'gene': {u'geneid': u'7157', u'symbol': u'TP53'},
u'hg19': {u'end': 7578533, u'start': 7578532},
u'ref': u'A',
u'rsid': u'rs28934873',
u'validated': False,
u'var_subtype': u'ts',
u'vartype': u'snp'},
u'mutdb': {u'alt': u'C',
u'chrom': u'17',
u'cosmic_id': u'43723',
u'hg19': {u'end': 7578532, u'start': 7578532},
u'mutpred_score': 0.74,
u'ref': u'T',
u'rsid': u'rs28934873',
u'strand': u'm'},
u'snpeff': {u'ann': [{u'cdna': {u'length': u'2271', u'position': u'280'},
u'cds': {u'length': u'786', u'position': u'2'},
u'effect': u'start_lost',
u'feature_id': u'NM_001126115.1',
u'feature_type': u'transcript',
u'gene_id': u'TP53',
u'gene_name': u'TP53',
u'hgvs_c': u'c.2T>C',
u'hgvs_p': u'p.Met1?',
u'protein': {u'length': u'261', u'position': u'1'},
u'putative_impact': u'HIGH',
u'rank': u'1',
u'total': u'7',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2404', u'position': u'280'},
u'cds': {u'length': u'630', u'position': u'2'},
u'effect': u'start_lost',
u'feature_id': u'NM_001126116.1',
u'feature_type': u'transcript',
u'gene_id': u'TP53',
u'gene_name': u'TP53',
u'hgvs_c': u'c.2T>C',
u'hgvs_p': u'p.Met1?',
u'protein': {u'length': u'209', u'position': u'1'},
u'putative_impact': u'HIGH',
u'rank': u'1',
u'total': u'8',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2331', u'position': u'280'},
u'cds': {u'length': u'645', u'position': u'2'},
u'effect': u'start_lost',
u'feature_id': u'NM_001126117.1',
u'feature_type': u'transcript',
u'gene_id': u'TP53',
u'gene_name': u'TP53',
u'hgvs_c': u'c.2T>C',
u'hgvs_p': u'p.Met1?',
u'protein': {u'length': u'214', u'position': u'1'},
u'putative_impact': u'HIGH',
u'rank': u'1',
u'total': u'8',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2591', u'position': u'600'},
u'cds': {u'length': u'1182', u'position': u'398'},
u'effect': u'missense_variant',
u'feature_id': u'NM_000546.5',
u'feature_type': u'transcript',
u'gene_id': u'TP53',
u'gene_name': u'TP53',
u'hgvs_c': u'c.398T>C',
u'hgvs_p': u'p.Met133Thr',
u'protein': {u'length': u'393', u'position': u'133'},
u'putative_impact': u'MODERATE',
u'rank': u'5',
u'total': u'11',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2588', u'position': u'597'},
u'cds': {u'length': u'1182', u'position': u'398'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001126112.2',
u'feature_type': u'transcript',
u'gene_id': u'TP53',
u'gene_name': u'TP53',
u'hgvs_c': u'c.398T>C',
u'hgvs_p': u'p.Met133Thr',
u'protein': {u'length': u'393', u'position': u'133'},
u'putative_impact': u'MODERATE',
u'rank': u'5',
u'total': u'11',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2651', u'position': u'600'},
u'cds': {u'length': u'1041', u'position': u'398'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001126113.2',
u'feature_type': u'transcript',
u'gene_id': u'TP53',
u'gene_name': u'TP53',
u'hgvs_c': u'c.398T>C',
u'hgvs_p': u'p.Met133Thr',
u'protein': {u'length': u'346', u'position': u'133'},
u'putative_impact': u'MODERATE',
u'rank': u'5',
u'total': u'12',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2724', u'position': u'600'},
u'cds': {u'length': u'1026', u'position': u'398'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001126114.2',
u'feature_type': u'transcript',
u'gene_id': u'TP53',
u'gene_name': u'TP53',
u'hgvs_c': u'c.398T>C',
u'hgvs_p': u'p.Met133Thr',
u'protein': {u'length': u'341', u'position': u'133'},
u'putative_impact': u'MODERATE',
u'rank': u'5',
u'total': u'12',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2708', u'position': u'717'},
u'cds': {u'length': u'1065', u'position': u'281'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001126118.1',
u'feature_type': u'transcript',
u'gene_id': u'TP53',
u'gene_name': u'TP53',
u'hgvs_c': u'c.281T>C',
u'hgvs_p': u'p.Met94Thr',
u'protein': {u'length': u'354', u'position': u'94'},
u'putative_impact': u'MODERATE',
u'rank': u'4',
u'total': u'10',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2651', u'position': u'600'},
u'cds': {u'length': u'924', u'position': u'281'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001276695.1',
u'feature_type': u'transcript',
u'gene_id': u'TP53',
u'gene_name': u'TP53',
u'hgvs_c': u'c.281T>C',
u'hgvs_p': u'p.Met94Thr',
u'protein': {u'length': u'307', u'position': u'94'},
u'putative_impact': u'MODERATE',
u'rank': u'5',
u'total': u'12',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2724', u'position': u'600'},
u'cds': {u'length': u'909', u'position': u'281'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001276696.1',
u'feature_type': u'transcript',
u'gene_id': u'TP53',
u'gene_name': u'TP53',
u'hgvs_c': u'c.281T>C',
u'hgvs_p': u'p.Met94Thr',
u'protein': {u'length': u'302', u'position': u'94'},
u'putative_impact': u'MODERATE',
u'rank': u'5',
u'total': u'12',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2591', u'position': u'600'},
u'cds': {u'length': u'1065', u'position': u'281'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001276760.1',
u'feature_type': u'transcript',
u'gene_id': u'TP53',
u'gene_name': u'TP53',
u'hgvs_c': u'c.281T>C',
u'hgvs_p': u'p.Met94Thr',
u'protein': {u'length': u'354', u'position': u'94'},
u'putative_impact': u'MODERATE',
u'rank': u'5',
u'total': u'11',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2588', u'position': u'597'},
u'cds': {u'length': u'1065', u'position': u'281'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001276761.1',
u'feature_type': u'transcript',
u'gene_id': u'TP53',
u'gene_name': u'TP53',
u'hgvs_c': u'c.281T>C',
u'hgvs_p': u'p.Met94Thr',
u'protein': {u'length': u'354', u'position': u'94'},
u'putative_impact': u'MODERATE',
u'rank': u'5',
u'total': u'11',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'80',
u'effect': u'5_prime_UTR_variant',
u'feature_id': u'NM_001276697.1',
u'feature_type': u'transcript',
u'gene_id': u'TP53',
u'gene_name': u'TP53',
u'hgvs_c': u'c.-80T>C',
u'putative_impact': u'MODIFIER',
u'rank': u'1',
u'total': u'7',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'80',
u'effect': u'5_prime_UTR_variant',
u'feature_id': u'NM_001276698.1',
u'feature_type': u'transcript',
u'gene_id': u'TP53',
u'gene_name': u'TP53',
u'hgvs_c': u'c.-80T>C',
u'putative_impact': u'MODIFIER',
u'rank': u'1',
u'total': u'8',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'80',
u'effect': u'5_prime_UTR_variant',
u'feature_id': u'NM_001276699.1',
u'feature_type': u'transcript',
u'gene_id': u'TP53',
u'gene_name': u'TP53',
u'hgvs_c': u'c.-80T>C',
u'putative_impact': u'MODIFIER',
u'rank': u'1',
u'total': u'8',
u'transcript_biotype': u'Coding'}],
u'lof': {u'gene_id': u'TP53',
u'gene_name': u'TP53',
u'number_of_transcripts_in_gene': u'15',
u'percent_of_transcripts_affected': u'0.20'}},
u'vcf': {u'alt': u'G', u'position': u'7578532', u'ref': u'A'}}],
u'max_score': 16.53367,
u'took': 21,
u'total': 1}
out = mv.query('clinvar.gene.symbol:BRCA1')
By default, the output lists the top 10 hits among 3532 unique variants recorded in ClinVar related to BRCA1. out
{u'hits': [{u'_id': u'NM_007294.3:c.4358-?_5277+?del',
u'_score': 12.69064,
u'clinvar': {u'allele_id': 94606,
u'chrom': u'17',
u'coding_hgvs_only': True,
u'cytogenic': u'17q21.31',
u'gene': {u'id': u'672', u'symbol': u'BRCA1'},
u'hgvs': {u'coding': [u'LRG_292t1:c.4358-?_5277+?del',
u'NM_007294.3:c.4358-?_5277+?del'],
u'genomic': [u'LRG_292:g.(?_141370_160932_?)del',
u'NC_000017.11:g.(?_43057052)_(43076614_?)del',
u'NC_000017.10:g.(?_41209069)_(41228631_?)del']},
u'rcv': [{u'accession': u'RCV000119187',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'identifiers': {u'medgen': u'C0677776'},
u'name': u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer (HBOC)',
u'synonyms': [u'q', u'Hereditary breast and ovarian cancer syndrome']},
u'last_evaluated': u'2014-03-27',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.4358-?_5277+?del',
u'review_status': u'no assertion criteria provided'},
{u'accession': u'RCV000074593',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'identifiers': {u'medgen': u'C0346153',
u'omim': u'114480'},
u'name': u'Familial cancer of breast',
u'synonyms': [u'CHEK2-Related Breast Cancer',
u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer']},
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.4358-?_5277+?del',
u'review_status': u'criteria provided, single submitter'}],
u'type': u'Deletion',
u'variant_id': 89063}},
{u'_id': u'chr17:g.41197590_41197593del',
u'_score': 12.69064,
u'clinvar': {u'allele_id': 102794,
u'alt': u'-',
u'chrom': u'17',
u'cytogenic': u'17q21.31',
u'gene': {u'id': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41197593, u'start': 41197590},
u'hg38': {u'end': 43045576, u'start': 43045573},
u'hgvs': {u'coding': [u'LRG_292t1:c.*102_*105delCTGT',
u'NM_007294.3:c.*102_*105delCTGT'],
u'genomic': [u'LRG_292:g.172408_172411delCTGT',
u'NG_005905.2:g.172408_172411delCTGT',
u'NC_000017.11:g.43045573_43045576delACAG',
u'NC_000017.10:g.41197590_41197593delACAG']},
u'rcv': {u'accession': u'RCV000083012',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'age_of_onset': u'All ages',
u'identifiers': {u'medgen': u'C2676676',
u'omim': u'604370',
u'orphanet': u'145'},
u'name': u'Breast-ovarian cancer, familial 1 (BROVCA1)',
u'synonyms': [u'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'OVARIAN CANCER, SUSCEPTIBILITY TO',
u'BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'Breast cancer, familial 1',
u'hereditary breast and ovarian cancer, BROVCA1',
u'Breast-ovarian cancer, familial, 1']},
u'last_evaluated': u'2011-10-17',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.*102_*105delCTGT',
u'review_status': u'no assertion criteria provided'},
u'ref': u'ACAG',
u'rsid': u'rs431825382',
u'type': u'Deletion',
u'variant_id': 96891},
u'snpeff': {u'ann': [{u'distance_to_feature': u'102',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007300.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*102_*105delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'24',
u'total': u'24',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'102',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007298.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*102_*105delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'102',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007297.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*102_*105delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'208',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007299.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*208_*211delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'102',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007294.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*102_*105delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'23',
u'total': u'23',
u'transcript_biotype': u'Coding'},
{u'effect': u'non_coding_exon_variant',
u'feature_id': u'NR_027676.1',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'n.5830_5833delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'23',
u'total': u'23',
u'transcript_biotype': u'Noncoding'}]},
u'vcf': {u'alt': u'G', u'position': u'41197589', u'ref': u'GACAG'}},
{u'_id': u'chr17:g.41197737C>G',
u'_score': 12.69064,
u'cadd': {u'_license': u'http://goo.gl/bkpNhq',
u'alt': u'G',
u'anc': u'C',
u'annotype': u'CodingTranscript',
u'bstatistic': 116,
u'chmm': {u'bivflnk': 0.0,
u'enh': 0.008,
u'enhbiv': 0.0,
u'het': 0.0,
u'quies': 0.299,
u'reprpc': 0.0,
u'reprpcwk': 0.0,
u'tssa': 0.0,
u'tssaflnk': 0.0,
u'tssbiv': 0.0,
u'tx': 0.205,
u'txflnk': 0.0,
u'txwk': 0.48,
u'znfrpts': 0.0},
u'chrom': 17,
u'consdetail': u'synonymous',
u'consequence': u'SYNONYMOUS',
u'consscore': 5,
u'cpg': 0.01,
u'dna': {u'helt': 1.78, u'mgw': 0.48, u'prot': -0.7, u'roll': -0.17},
u'encode': {u'exp': 371.32,
u'h3k27ac': 12.76,
u'h3k4me1': 3.0,
u'h3k4me3': 3.0,
u'nucleo': 1.3},
u'exon': u'24/24',
u'fitcons': 0.723164,
u'gc': 0.6,
u'gene': {u'ccds_id': u'CCDS11456.2',
u'cds': {u'cdna_pos': 5845,
u'cds_pos': 5613,
u'rel_cdna_pos': 0.98,
u'rel_cds_pos': 0.99},
u'feature_id': u'ENST00000471181',
u'gene_id': u'ENSG00000012048',
u'genename': u'BRCA1',
u'prot': {u'domain': u'ndomain',
u'protpos': 1871,
u'rel_prot_pos': 0.99}},
u'gerp': {u'n': 5.32, u'rs': 844.9, u'rs_pval': 8.78912e-51, u's': 4.33},
u'isderived': u'TRUE',
u'isknownvariant': u'FALSE',
u'istv': u'TRUE',
u'length': 0,
u'mapability': {u'20bp': 0.5, u'35bp': 1},
u'min_dist_tse': 42,
u'min_dist_tss': 78396,
u'mirsvr': {u'aln': 148, u'e': -24.01, u'score': -0.2148},
u'mutindex': 8,
u'naa': u'L',
u'oaa': u'L',
u'phast_cons': {u'mammalian': 1.0, u'primate': 0.997, u'vertebrate': 1.0},
u'phred': 12.85,
u'phylop': {u'mammalian': 2.766, u'primate': 0.559, u'vertebrate': 1.674},
u'pos': 41197737,
u'rawscore': 1.4117,
u'ref': u'C',
u'segway': u'TF2',
u'type': u'SNV'},
u'clinvar': {u'allele_id': 184867,
u'alt': u'G',
u'chrom': u'17',
u'cytogenic': u'17q21.31',
u'gene': {u'id': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41197737, u'start': 41197737},
u'hg38': {u'end': 43045720, u'start': 43045720},
u'hgvs': {u'coding': [u'LRG_292t1:c.5550G>C',
u'NM_007299.3:c.*64G>C',
u'NM_007294.3:c.5550G>C'],
u'genomic': [u'LRG_292:g.172264G>C',
u'NG_005905.2:g.172264G>C',
u'NC_000017.11:g.43045720C>G',
u'NC_000017.10:g.41197737C>G']},
u'rcv': {u'accession': u'RCV000163767',
u'clinical_significance': u'Likely benign',
u'conditions': {u'identifiers': {u'medgen': u'C0027672'},
u'name': u'Hereditary cancer-predisposing syndrome',
u'synonyms': u'Neoplastic Syndromes, Hereditary'},
u'last_evaluated': u'2013-12-19',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5550G>C (p.Leu1850=)',
u'review_status': u'criteria provided, single submitter'},
u'ref': u'C',
u'rsid': u'rs786201502',
u'type': u'single nucleotide variant',
u'variant_id': 184500},
u'snpeff': {u'ann': [{u'cdna': {u'length': u'7270', u'position': u'5845'},
u'cds': {u'length': u'5655', u'position': u'5613'},
u'effect': u'synonymous_variant',
u'feature_id': u'NM_007300.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5613G>C',
u'hgvs_p': u'p.Leu1871Leu',
u'protein': {u'length': u'1884', u'position': u'1871'},
u'putative_impact': u'LOW',
u'rank': u'24',
u'total': u'24',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'3682', u'position': u'2257'},
u'cds': {u'length': u'2280', u'position': u'2238'},
u'effect': u'synonymous_variant',
u'feature_id': u'NM_007298.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.2238G>C',
u'hgvs_p': u'p.Leu746Leu',
u'protein': {u'length': u'759', u'position': u'746'},
u'putative_impact': u'LOW',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'7115', u'position': u'5690'},
u'cds': {u'length': u'5451', u'position': u'5409'},
u'effect': u'synonymous_variant',
u'feature_id': u'NM_007297.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5409G>C',
u'hgvs_p': u'p.Leu1803Leu',
u'protein': {u'length': u'1816', u'position': u'1803'},
u'putative_impact': u'LOW',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'7207', u'position': u'5782'},
u'cds': {u'length': u'5592', u'position': u'5550'},
u'effect': u'synonymous_variant',
u'feature_id': u'NM_007294.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5550G>C',
u'hgvs_p': u'p.Leu1850Leu',
u'protein': {u'length': u'1863', u'position': u'1850'},
u'putative_impact': u'LOW',
u'rank': u'23',
u'total': u'23',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'64',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007299.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*64G>C',
u'putative_impact': u'MODIFIER',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'effect': u'non_coding_exon_variant',
u'feature_id': u'NR_027676.1',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'n.5686G>C',
u'putative_impact': u'MODIFIER',
u'rank': u'23',
u'total': u'23',
u'transcript_biotype': u'Noncoding'}]},
u'vcf': {u'alt': u'G', u'position': u'41197737', u'ref': u'C'}},
{u'_id': u'chr17:g.41197776C>T',
u'_score': 12.69064,
u'cadd': {u'_license': u'http://goo.gl/bkpNhq',
u'alt': u'T',
u'anc': u'C',
u'annotype': u'CodingTranscript',
u'bstatistic': 116,
u'chmm': {u'bivflnk': 0.0,
u'enh': 0.008,
u'enhbiv': 0.0,
u'het': 0.0,
u'quies': 0.299,
u'reprpc': 0.0,
u'reprpcwk': 0.0,
u'tssa': 0.0,
u'tssaflnk': 0.0,
u'tssbiv': 0.0,
u'tx': 0.205,
u'txflnk': 0.0,
u'txwk': 0.48,
u'znfrpts': 0.0},
u'chrom': 17,
u'consdetail': u'stop_gained',
u'consequence': u'STOP_GAINED',
u'consscore': 8,
u'cpg': 0.01,
u'dna': {u'helt': 1.68, u'mgw': 0.28, u'prot': -2.32, u'roll': 0.2},
u'encode': {u'exp': 383.33,
u'h3k27ac': 11.52,
u'h3k4me1': 4.0,
u'h3k4me3': 2.56,
u'nucleo': 3.3},
u'exon': u'24/24',
u'fitcons': 0.723164,
u'gc': 0.56,
u'gene': {u'ccds_id': u'CCDS11456.2',
u'cds': {u'cdna_pos': 5806,
u'cds_pos': 5574,
u'rel_cdna_pos': 0.98,
u'rel_cds_pos': 0.99},
u'feature_id': u'ENST00000471181',
u'gene_id': u'ENSG00000012048',
u'genename': u'BRCA1',
u'prot': {u'domain': u'ndomain',
u'protpos': 1858,
u'rel_prot_pos': 0.99}},
u'gerp': {u'n': 5.32, u'rs': 844.9, u'rs_pval': 8.78912e-51, u's': 5.32},
u'isderived': u'TRUE',
u'isknownvariant': u'FALSE',
u'istv': u'FALSE',
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u'mapability': {u'20bp': 1, u'35bp': 1},
u'min_dist_tse': 81,
u'min_dist_tss': 78357,
u'mirsvr': {u'aln': 127, u'e': -21.58, u'score': -0.1772},
u'mutindex': 41,
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u'phast_cons': {u'mammalian': 1.0, u'primate': 0.997, u'vertebrate': 1.0},
u'phred': 49,
u'phylop': {u'mammalian': 2.766, u'primate': 0.559, u'vertebrate': 3.085},
u'pos': 41197776,
u'rawscore': 15.183713,
u'ref': u'C',
u'segway': u'TF2',
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u'clinvar': {u'allele_id': 70276,
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u'chrom': u'17',
u'cytogenic': u'17q21.31',
u'gene': {u'id': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41197776, u'start': 41197776},
u'hg38': {u'end': 43045759, u'start': 43045759},
u'hgvs': {u'coding': [u'LRG_292t1:c.5511G>A',
u'NM_007299.3:c.*25G>A',
u'NM_007294.3:c.5511G>A'],
u'genomic': [u'LRG_292:g.172225G>A',
u'NG_005905.2:g.172225G>A',
u'NC_000017.11:g.43045759C>T',
u'NC_000017.10:g.41197776C>T']},
u'rcv': [{u'accession': u'RCV000049029',
u'clinical_significance': u'not provided',
u'conditions': {u'identifiers': {u'medgen': u'C0346153',
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u'name': u'Familial cancer of breast',
u'synonyms': [u'CHEK2-Related Breast Cancer',
u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer']},
u'last_evaluated': u'2013-02-01',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5511G>A (p.Trp1837Ter)',
u'review_status': u'no assertion provided'},
{u'accession': u'RCV000112692',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'age_of_onset': u'All ages',
u'identifiers': {u'medgen': u'C2676676',
u'omim': u'604370',
u'orphanet': u'145'},
u'name': u'Breast-ovarian cancer, familial 1 (BROVCA1)',
u'synonyms': [u'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'OVARIAN CANCER, SUSCEPTIBILITY TO',
u'BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'Breast cancer, familial 1',
u'hereditary breast and ovarian cancer, BROVCA1',
u'Breast-ovarian cancer, familial, 1']},
u'last_evaluated': u'2006-07-19',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5511G>A (p.Trp1837Ter)',
u'review_status': u'no assertion criteria provided'}],
u'ref': u'C',
u'rsid': u'rs80356914',
u'type': u'single nucleotide variant',
u'variant_id': 55609},
u'dbnsfp': {u'aa': {u'alt': u'X',
u'codonpos': 3,
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u'147',
u'328',
u'70',
u'1790',
u'1858',
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u'cds_strand': u'-',
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u'clinvar': {u'clinsig': 5,
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u'trait': u'Breast-ovarian_cancer\\x2c_familial_1'},
u'ensembl': {u'geneid': u'ENSG00000012048',
u'proteinid': [u'ENSP00000350283',
u'ENSP00000312236',
u'ENSP00000465818',
u'ENSP00000467329',
u'ENSP00000465347',
u'ENSP00000418775',
u'ENSP00000418960',
u'ENSP00000420705'],
u'transcriptid': [u'ENST00000357654',
u'ENST00000352993',
u'ENST00000586385',
u'ENST00000591534',
u'ENST00000591849',
u'ENST00000493795',
u'ENST00000471181',
u'ENST00000491747']},
u'fathmm-mkl': {u'coding_group': u'AEFBI',
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u'coding_score': 0.91246},
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u'gerp++': {u'nr': 5.32, u'rs': 5.32, u'rs_rankscore': 0.75224},
u'gm12878': {u'confidence_value': 0,
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u'h1-hesc': {u'confidence_value': 0,
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u'fitcons_score': 0.743671},
u'hg18': {u'end': 38451302, u'start': 38451302},
u'hg19': {u'end': 41197776, u'start': 41197776},
u'hg38': {u'end': 43045759, u'start': 43045759},
u'huvec': {u'confidence_value': 0,
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u'fitcons_score': 0.714379},
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u'interpro_domain': u'BRCT domain',
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u'mutationtaster': {u'AAE': [u'W695*',
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u'W654*',
u'W686*',
u'W1541*',
u'W1837*',
u'W147*',
u'W328*',
u'W70*',
u'W1790*',
u'W1858*',
u'W733*',
u'W1572*',
u'.'],
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u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
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u'mammalian_rankscore': 0.48811},
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u'ref': u'C',
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u'pi': {u'a': 0.0, u'c': 1.0, u'g': 0.0, u't': 0.0}}},
u'dbsnp': {u'allele_origin': u'unspecified',
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u'alt': u'T',
u'chrom': u'17',
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u'dbsnp_build': 132,
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u'PM',
u'REF',
u'RV',
u'S3D',
u'SLO',
u'U3'],
u'gene': {u'geneid': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41197777, u'start': 41197776},
u'ref': u'C',
u'rsid': u'rs80356914',
u'validated': False,
u'var_subtype': u'unknown',
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u'snpeff': {u'ann': [{u'cdna': {u'length': u'7270', u'position': u'5806'},
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u'effect': u'stop_gained',
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u'gene_name': u'BRCA1',
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u'protein': {u'length': u'1884', u'position': u'1858'},
u'putative_impact': u'HIGH',
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u'feature_id': u'NM_007298.3',
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u'gene_id': u'BRCA1',
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u'hgvs_c': u'c.2199G>A',
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u'hgvs_c': u'c.5370G>A',
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u'cds': {u'length': u'5592', u'position': u'5511'},
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u'hgvs_p': u'p.Trp1837*',
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u'transcript_biotype': u'Coding'},
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{u'effect': u'non_coding_exon_variant',
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u'vcf': {u'alt': u'T', u'position': u'41197776', u'ref': u'C'}},
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u'cadd': {u'_license': u'http://goo.gl/bkpNhq',
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u'annotype': u'CodingTranscript',
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u'grantham': 21,
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u'rcv': [{u'accession': u'RCV000049017',
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u'Breast cancer, familial 1',
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u'preferred_name': u'NM_007294.3(BRCA1):c.5497G>A (p.Val1833Met)',
u'review_status': u'no assertion criteria provided'},
{u'accession': u'RCV000132307',
u'clinical_significance': u'Likely pathogenic',
u'conditions': {u'identifiers': {u'medgen': u'C0027672'},
u'name': u'Hereditary cancer-predisposing syndrome',
u'synonyms': u'Neoplastic Syndromes, Hereditary'},
u'last_evaluated': u'2014-05-02',
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u'ref': u'C',
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u'dbnsfp': {u'aa': {u'alt': u'M',
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u'143',
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u'66',
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u'1854',
u'729'],
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u'chrom': u'17',
u'clinvar': {u'clinsig': 4,
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u'trait': u'Hereditary_cancer-predisposing_syndrome'},
u'ensembl': {u'geneid': u'ENSG00000012048',
u'proteinid': [u'ENSP00000350283',
u'ENSP00000312236',
u'ENSP00000465818',
u'ENSP00000467329',
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u'ENSP00000418775',
u'ENSP00000418960',
u'ENSP00000420705'],
u'transcriptid': [u'ENST00000357654',
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u'ENST00000586385',
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u'ENST00000591849',
u'ENST00000493795',
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u'fathmm': {u'pred': [u'D', u'D', u'D', u'D', u'D', u'D', u'D', u'D'],
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u'score': [-3.68, -3.68, -3.68, -3.68, -3.68, -3.68, -3.68, -3.68]},
u'fathmm-mkl': {u'coding_group': u'AEFBI',
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u'gm12878': {u'confidence_value': 0,
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u'h1-hesc': {u'confidence_value': 0,
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u'fitcons_score': 0.743671},
u'hg18': {u'end': 38451316, u'start': 38451316},
u'hg19': {u'end': 41197790, u'start': 41197790},
u'hg38': {u'end': 43045773, u'start': 43045773},
u'huvec': {u'confidence_value': 0,
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u'fitcons_score': 0.635551},
u'integrated': {u'confidence_value': 0,
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u'fitcons_score': 0.732398},
u'interpro_domain': u'BRCT domain',
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u'omega': 0.0,
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u'metalr': {u'pred': u'D', u'rankscore': 0.96404, u'score': 0.8916},
u'metasvm': {u'pred': u'D', u'rankscore': 0.96424, u'score': 0.9519},
u'mutationassessor': {u'pred': u'M',
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u'score': 2.215},
u'mutationtaster': {u'AAE': [u'V1833M',
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u'V324M',
u'V66M',
u'V1786M',
u'V1854M',
u'V729M',
u'V691M',
u'V650M',
u'V682M',
u'V1537M',
u'.',
u'V1568M',
u'V1594M'],
u'converted_rankscore': 0.81033,
u'model': [u'simple_aae',
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u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
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u'D',
u'D',
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u'D',
u'D',
u'D',
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u'D',
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0.999766,
0.999766,
0.999766,
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0.99859,
0.999766,
0.999766,
0.999766,
0.999766,
0.99766,
1,
0.897669,
0.897669]},
u'phastcons': {u'20way': {u'mammalian': 0.86,
u'mammalian_rankscore': 0.35735},
u'7way': {u'vertebrate': 0.976, u'vertebrate_rankscore': 0.4664}},
u'phylo': {u'p20way': {u'mammalian': 0.935,
u'mammalian_rankscore': 0.48811},
u'p7way': {u'vertebrate': 0.871, u'vertebrate_rankscore': 0.44667}},
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u'score': 1.0},
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u'alt': u'T',
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u'PM',
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u'S3D',
u'SLO',
u'U3'],
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u'hg19': {u'end': 41197791, u'start': 41197790},
u'ref': u'C',
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u'validated': False,
u'var_subtype': u'ts',
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u'mutdb': {u'alt': u'A',
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u'mutpred_score': 0.585,
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u'hgvs_p': u'p.Val1833Met',
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u'h3k4me3': 2.0,
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u'exon': u'24/24',
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u'feature_id': u'ENST00000471181',
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u'grantham': 29,
u'isderived': u'TRUE',
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u'mapability': {u'20bp': 1, u'35bp': 1},
u'min_dist_tse': 122,
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u'mutindex': 13,
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u'rawscore': 2.821365,
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u'clinvar': {u'allele_id': 151518,
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u'hg38': {u'end': 43045800, u'start': 43045800},
u'hgvs': {u'coding': [u'LRG_292t1:c.5470A>G', u'NM_007294.3:c.5470A>G'],
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u'NC_000017.11:g.43045800T>C',
u'NC_000017.10:g.41197817T>C']},
u'rcv': [{u'accession': u'RCV000130459',
u'clinical_significance': u'Uncertain significance',
u'conditions': {u'identifiers': {u'medgen': u'C0027672'},
u'name': u'Hereditary cancer-predisposing syndrome',
u'synonyms': u'Neoplastic Syndromes, Hereditary'},
u'last_evaluated': u'2013-10-15',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5470A>G (p.Ile1824Val)',
u'review_status': u'criteria provided, single submitter'},
{u'accession': u'RCV000168345',
u'clinical_significance': u'Uncertain significance',
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u'last_evaluated': u'2014-12-18',
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u'ref': u'T',
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u'dbnsfp': {u'aa': [{u'alt': u'V',
u'codonpos': 1,
u'pos': [u'1824',
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u'315',
u'57',
u'1777',
u'1845',
u'720'],
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u'ref': u'N',
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u'alt': u'C',
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u'cds_strand': u'-',
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u'ensembl': {u'geneid': u'ENSG00000012048',
u'proteinid': [u'ENSP00000350283',
u'ENSP00000312236',
u'ENSP00000465818',
u'ENSP00000467329',
u'ENSP00000465347',
u'ENSP00000418775',
u'ENSP00000418960',
u'ENSP00000420705'],
u'transcriptid': [u'ENST00000357654',
u'ENST00000352993',
u'ENST00000586385',
u'ENST00000591534',
u'ENST00000591849',
u'ENST00000493795',
u'ENST00000471181',
u'ENST00000491747']},
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u'coding_score': 0.66377},
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u'gm12878': {u'confidence_value': 0,
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u'fitcons_score': 0.724815},
u'h1-hesc': {u'confidence_value': 0,
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u'fitcons_score': 0.643519},
u'hg18': {u'end': 38451343, u'start': 38451343},
u'hg19': {u'end': 41197817, u'start': 41197817},
u'hg38': {u'end': 43045800, u'start': 43045800},
u'huvec': {u'confidence_value': 0,
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u'fitcons_score': 0.683762},
u'integrated': {u'confidence_value': 0,
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u'fitcons_score': 0.706548},
u'interpro_domain': u'BRCT domain',
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u'mutationassessor': {u'pred': u'L', u'rankscore': 0.54432, u'score': 1.7},
u'mutationtaster': {u'AAE': [u'I1824V',
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u'I134V',
u'I315V',
u'I57V',
u'I1777V',
u'I1845V',
u'I720V',
u'I1559V',
u'I682V',
u'I1585V',
u'I641V',
u'I673V',
u'I1528V'],
u'converted_rankscore': 0.20894,
u'model': [u'simple_aae',
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u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
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u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae'],
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0.999593,
0.999833,
0.999973,
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1,
0.999834,
1,
0.999834,
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0.999983]},
u'phastcons': {u'20way': {u'mammalian': 0.995,
u'mammalian_rankscore': 0.60234},
u'7way': {u'vertebrate': 0.958, u'vertebrate_rankscore': 0.42521}},
u'phylo': {u'p20way': {u'mammalian': 1.061,
u'mammalian_rankscore': 0.80647},
u'p7way': {u'vertebrate': 0.991, u'vertebrate_rankscore': 0.76621}},
u'polyphen2': {u'hdiv': {u'pred': [u'P', u'B', u'P', u'P', u'P', u'P'],
u'rankscore': 0.49299,
u'score': [0.924, 0.021, 0.653, 0.884, 0.884, 0.75]},
u'hvar': {u'pred': [u'D', u'B', u'P', u'P', u'P', u'B'],
u'rankscore': 0.68618,
u'score': [0.96, 0.015, 0.452, 0.606, 0.606, 0.323]}},
u'provean': {u'pred': [u'N', u'N', u'.', u'.', u'.', u'N', u'.', u'N'],
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u'score': [-0.18, -0.67, None, None, None, -0.18, None, -0.66]},
u'ref': u'T',
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u'uniprot': [{u'acc': u'B4DES0', u'pos': u'673'},
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{u'acc': u'P38398', u'pos': u'1824'},
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u'dbsnp': {u'allele_origin': u'unspecified',
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u'alt': u'C',
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u'hg19': {u'end': 41197818, u'start': 41197817},
u'ref': u'T',
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u'validated': False,
u'var_subtype': u'ts',
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u'snpeff': {u'ann': [{u'cdna': {u'length': u'7270', u'position': u'5765'},
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u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5533A>G',
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u'putative_impact': u'MODERATE',
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u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.2158A>G',
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u'gene_name': u'BRCA1',
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u'putative_impact': u'MODERATE',
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u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.2084A>G',
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u'vcf': {u'alt': u'C', u'position': u'41197817', u'ref': u'T'}},
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u'cadd': {u'_license': u'http://goo.gl/bkpNhq',
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u'chrom': 17,
u'consdetail': u'stop_gained',
u'consequence': u'STOP_GAINED',
u'consscore': 8,
u'cpg': 0.0,
u'dna': {u'helt': -2.25, u'mgw': 0.1, u'prot': 1.39, u'roll': -0.69},
u'encode': {u'exp': 244.65,
u'h3k27ac': 5.0,
u'h3k4me1': 3.0,
u'h3k4me3': 5.04,
u'nucleo': 2.3},
u'exon': u'23/24',
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u'gc': 0.52,
u'gene': {u'ccds_id': u'CCDS11456.2',
u'cds': {u'cdna_pos': 5726,
u'cds_pos': 5494,
u'rel_cdna_pos': 0.96,
u'rel_cds_pos': 0.97},
u'feature_id': u'ENST00000471181',
u'gene_id': u'ENSG00000012048',
u'genename': u'BRCA1',
u'prot': {u'domain': u'ndomain',
u'protpos': 1832,
u'rel_prot_pos': 0.97}},
u'gerp': {u'n': 4.98, u'rs': 137.8, u'rs_pval': 2.45126e-14, u's': 4},
u'isderived': u'TRUE',
u'isknownvariant': u'FALSE',
u'istv': u'FALSE',
u'length': 0,
u'mapability': {u'20bp': 1, u'35bp': 1},
u'min_dist_tse': 2001,
u'min_dist_tss': 76437,
u'mutindex': -1,
u'naa': u'*',
u'oaa': u'Q',
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u'primate': 0.972,
u'vertebrate': 0.994},
u'phred': 42,
u'phylop': {u'mammalian': 1.291, u'primate': 0.457, u'vertebrate': 1.579},
u'pos': 41199696,
u'rawscore': 13.523835,
u'ref': u'G',
u'segway': u'GE1',
u'type': u'SNV'},
u'clinvar': {u'allele_id': 70244,
u'alt': u'A',
u'chrom': u'17',
u'cytogenic': u'17q21.31',
u'gene': {u'id': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41199696, u'start': 41199696},
u'hg38': {u'end': 43047679, u'start': 43047679},
u'hgvs': {u'coding': [u'LRG_292t1:c.5431C>T',
u'NM_007299.3:c.2045C>T',
u'NM_007294.3:c.5431C>T'],
u'genomic': [u'LRG_292:g.170305C>T',
u'NG_005905.2:g.170305C>T',
u'NC_000017.11:g.43047679G>A',
u'NC_000017.10:g.41199696G>A']},
u'rcv': {u'accession': u'RCV000048992',
u'clinical_significance': u'not provided',
u'conditions': {u'identifiers': {u'medgen': u'C0346153',
u'omim': u'114480'},
u'name': u'Familial cancer of breast',
u'synonyms': [u'CHEK2-Related Breast Cancer',
u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer']},
u'last_evaluated': u'2013-02-01',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5431C>T (p.Gln1811Ter)',
u'review_status': u'no assertion provided'},
u'ref': u'G',
u'rsid': u'rs397509283',
u'type': u'single nucleotide variant',
u'variant_id': 55577},
u'dbnsfp': {u'aa': [{u'alt': u'V',
u'codonpos': 2,
u'pos': 682,
u'ref': u'A',
u'refcodon': u'GCA'},
{u'alt': u'X',
u'codonpos': 1,
u'pos': [u'1811',
u'669',
u'121',
u'302',
u'44',
u'1764',
u'1832',
u'707'],
u'ref': u'Q',
u'refcodon': u'CAG'}],
u'alt': u'A',
u'ancestral_allele': u'G',
u'cds_strand': u'-',
u'chrom': u'17',
u'ensembl': {u'geneid': u'ENSG00000012048',
u'proteinid': u'ENSP00000417148',
u'transcriptid': u'ENST00000468300'},
u'fathmm': {u'pred': u'D', u'rankscore': 0.86976, u'score': -2.21},
u'fathmm-mkl': {u'coding_group': u'AEFBI',
u'coding_pred': u'D',
u'coding_rankscore': 0.40267,
u'coding_score': 0.81078},
u'genename': u'BRCA1',
u'gerp++': {u'nr': 4.98, u'rs': 4.0, u'rs_rankscore': 0.45405},
u'gm12878': {u'confidence_value': 0,
u'fitcons_rankscore': 0.89268,
u'fitcons_score': 0.724815},
u'h1-hesc': {u'confidence_value': 0,
u'fitcons_rankscore': 0.87815,
u'fitcons_score': 0.724815},
u'hg18': {u'end': 38453222, u'start': 38453222},
u'hg19': {u'end': 41199696, u'start': 41199696},
u'hg38': {u'end': 43047679, u'start': 43047679},
u'huvec': {u'confidence_value': 0,
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u'fitcons_score': 0.714379},
u'integrated': {u'confidence_value': 0,
u'fitcons_rankscore': 0.72903,
u'fitcons_score': 0.706548},
u'metalr': {u'pred': u'T', u'rankscore': 0.6989, u'score': 0.331},
u'metasvm': {u'pred': u'T', u'rankscore': 0.73054, u'score': -0.3676},
u'mutationtaster': {u'AAE': [u'Q1811*',
u'Q121*',
u'Q302*',
u'Q44*',
u'Q1764*',
u'Q1832*',
u'Q707*',
u'Q1546*',
u'Q669*',
u'Q1572*',
u'Q628*',
u'Q660*',
u'Q1515*',
u'A682V'],
u'converted_rankscore': 0.81033,
u'model': [u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'simple_aae'],
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u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
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u'D',
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u'N'],
u'score': [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.998828]},
u'phastcons': {u'20way': {u'mammalian': 0.979,
u'mammalian_rankscore': 0.48478},
u'7way': {u'vertebrate': 0.738, u'vertebrate_rankscore': 0.30575}},
u'phylo': {u'p20way': {u'mammalian': 0.949,
u'mammalian_rankscore': 0.53485},
u'p7way': {u'vertebrate': 0.917, u'vertebrate_rankscore': 0.60462}},
u'polyphen2': {u'hdiv': {u'pred': u'P',
u'rankscore': 0.42763,
u'score': 0.793},
u'hvar': {u'pred': u'B', u'rankscore': 0.37443, u'score': 0.254}},
u'provean': {u'pred': u'N', u'rankscore': 0.12864, u'score': -0.35},
u'ref': u'G',
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u'rsid': u'rs397509283',
u'sift': {u'converted_rankscore': 0.91219, u'pred': u'D', u'score': 0.0},
u'siphy_29way': {u'logodds': 11.2065,
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u'pi': {u'a': 0.0, u'c': 0.185, u'g': 0.815, u't': 0.0}},
u'uniprot': {u'acc': u'Q6IN79', u'pos': u'682'}},
u'dbsnp': {u'allele_origin': u'unspecified',
u'alleles': [{u'allele': u'G'}, {u'allele': u'A'}],
u'alt': u'A',
u'chrom': u'17',
u'class': u'SNV',
u'dbsnp_build': 136,
u'flags': [u'ASP', u'LSD', u'NSM', u'NSN', u'PM', u'REF', u'RV'],
u'gene': {u'geneid': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41199697, u'start': 41199696},
u'ref': u'G',
u'rsid': u'rs397509283',
u'validated': False,
u'var_subtype': u'ts',
u'vartype': u'snp'},
u'snpeff': {u'ann': [{u'cdna': {u'length': u'7270', u'position': u'5726'},
u'cds': {u'length': u'5655', u'position': u'5494'},
u'effect': u'stop_gained',
u'feature_id': u'NM_007300.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5494C>T',
u'hgvs_p': u'p.Gln1832*',
u'protein': {u'length': u'1884', u'position': u'1832'},
u'putative_impact': u'HIGH',
u'rank': u'23',
u'total': u'24',
u'transcript_biotype': u'Coding'},
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u'cds': {u'length': u'2280', u'position': u'2119'},
u'effect': u'stop_gained',
u'feature_id': u'NM_007298.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.2119C>T',
u'hgvs_p': u'p.Gln707*',
u'protein': {u'length': u'759', u'position': u'707'},
u'putative_impact': u'HIGH',
u'rank': u'21',
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u'transcript_biotype': u'Coding'},
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u'cds': {u'length': u'5451', u'position': u'5290'},
u'effect': u'stop_gained',
u'feature_id': u'NM_007297.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5290C>T',
u'hgvs_p': u'p.Gln1764*',
u'protein': {u'length': u'1816', u'position': u'1764'},
u'putative_impact': u'HIGH',
u'rank': u'21',
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u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'7207', u'position': u'5663'},
u'cds': {u'length': u'5592', u'position': u'5431'},
u'effect': u'stop_gained',
u'feature_id': u'NM_007294.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5431C>T',
u'hgvs_p': u'p.Gln1811*',
u'protein': {u'length': u'1863', u'position': u'1811'},
u'putative_impact': u'HIGH',
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u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'3783', u'position': u'2239'},
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u'effect': u'missense_variant',
u'feature_id': u'NM_007299.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.2045C>T',
u'hgvs_p': u'p.Ala682Val',
u'protein': {u'length': u'699', u'position': u'682'},
u'putative_impact': u'MODERATE',
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u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'effect': u'non_coding_exon_variant',
u'feature_id': u'NR_027676.1',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'n.5567C>T',
u'putative_impact': u'MODIFIER',
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u'transcript_biotype': u'Noncoding'}]},
u'vcf': {u'alt': u'A', u'position': u'41199696', u'ref': u'G'}},
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u'cadd': {u'_license': u'http://goo.gl/bkpNhq',
u'alt': u'T',
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u'annotype': u'CodingTranscript',
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u'chmm': {u'bivflnk': 0.0,
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u'quies': 0.276,
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u'txwk': 0.512,
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u'chrom': 17,
u'consdetail': u'synonymous',
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u'dna': {u'helt': 1.15, u'mgw': 0.36, u'prot': -2.73, u'roll': 1.13},
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u'isderived': u'TRUE',
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u'min_dist_tse': 2002,
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u'mutindex': 8,
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u'rawscore': 1.929904,
u'ref': u'C',
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u'clinvar': {u'allele_id': 184870,
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u'hg19': {u'end': 41199697, u'start': 41199697},
u'hg38': {u'end': 43047680, u'start': 43047680},
u'hgvs': {u'coding': [u'LRG_292t1:c.5430G>A',
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u'NG_005905.2:g.170304G>A',
u'NC_000017.11:g.43047680C>T',
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u'rcv': {u'accession': u'RCV000163918',
u'clinical_significance': u'Likely benign',
u'conditions': {u'identifiers': {u'medgen': u'C0027672'},
u'name': u'Hereditary cancer-predisposing syndrome',
u'synonyms': u'Neoplastic Syndromes, Hereditary'},
u'last_evaluated': u'2014-10-24',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5430G>A (p.Val1810=)',
u'review_status': u'criteria provided, single submitter'},
u'ref': u'C',
u'rsid': u'rs786201582',
u'type': u'single nucleotide variant',
u'variant_id': 184631},
u'dbnsfp': {u'aa': {u'alt': u'T',
u'codonpos': 1,
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u'ref': u'A',
u'refcodon': u'GCA'},
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u'ensembl': {u'geneid': u'ENSG00000012048',
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u'fathmm': {u'pred': u'D', u'rankscore': 0.87129, u'score': -2.23},
u'fathmm-mkl': {u'coding_group': u'AEFBI',
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u'coding_score': 0.60024},
u'genename': u'BRCA1',
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u'gm12878': {u'confidence_value': 0,
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u'fitcons_score': 0.724815},
u'h1-hesc': {u'confidence_value': 0,
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u'fitcons_score': 0.724815},
u'hg18': {u'end': 38453223, u'start': 38453223},
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u'hg38': {u'end': 43047680, u'start': 43047680},
u'huvec': {u'confidence_value': 0,
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u'fitcons_score': 0.714379},
u'integrated': {u'confidence_value': 0,
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u'fitcons_score': 0.706548},
u'metalr': {u'pred': u'T', u'rankscore': 0.78534, u'score': 0.451},
u'metasvm': {u'pred': u'T', u'rankscore': 0.70167, u'score': -0.4577},
u'mutationtaster': {u'AAE': [u'.', u'A682T'],
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u'model': [u'without_aae', u'simple_aae'],
u'pred': [u'D', u'N'],
u'score': [1, 0.999882]},
u'phastcons': {u'20way': {u'mammalian': 0.965,
u'mammalian_rankscore': 0.44841},
u'7way': {u'vertebrate': 0.72, u'vertebrate_rankscore': 0.30132}},
u'phylo': {u'p20way': {u'mammalian': 0.848,
u'mammalian_rankscore': 0.34552},
u'p7way': {u'vertebrate': 0.871, u'vertebrate_rankscore': 0.44667}},
u'polyphen2': {u'hdiv': {u'pred': u'B',
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u'score': 0.093},
u'hvar': {u'pred': u'B', u'rankscore': 0.18147, u'score': 0.021}},
u'provean': {u'pred': u'N', u'rankscore': 0.0439, u'score': 0.26},
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u'reliability_index': 8,
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u'siphy_29way': {u'logodds': 6.8927,
u'logodds_rankscore': 0.23194,
u'pi': {u'a': 0.0, u'c': 0.7216, u'g': 0.0, u't': 0.2784}},
u'uniprot': {u'acc': u'Q6IN79', u'pos': u'682'}},
u'snpeff': {u'ann': [{u'cdna': {u'length': u'3783', u'position': u'2238'},
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u'effect': u'missense_variant',
u'feature_id': u'NM_007299.3',
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u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.2044G>A',
u'hgvs_p': u'p.Ala682Thr',
u'protein': {u'length': u'699', u'position': u'682'},
u'putative_impact': u'MODERATE',
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u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'7270', u'position': u'5725'},
u'cds': {u'length': u'5655', u'position': u'5493'},
u'effect': u'synonymous_variant',
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u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5493G>A',
u'hgvs_p': u'p.Val1831Val',
u'protein': {u'length': u'1884', u'position': u'1831'},
u'putative_impact': u'LOW',
u'rank': u'23',
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u'transcript_biotype': u'Coding'},
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u'effect': u'synonymous_variant',
u'feature_id': u'NM_007298.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.2118G>A',
u'hgvs_p': u'p.Val706Val',
u'protein': {u'length': u'759', u'position': u'706'},
u'putative_impact': u'LOW',
u'rank': u'21',
u'total': u'22',
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{u'cdna': {u'length': u'7115', u'position': u'5570'},
u'cds': {u'length': u'5451', u'position': u'5289'},
u'effect': u'synonymous_variant',
u'feature_id': u'NM_007297.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5289G>A',
u'hgvs_p': u'p.Val1763Val',
u'protein': {u'length': u'1816', u'position': u'1763'},
u'putative_impact': u'LOW',
u'rank': u'21',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'7207', u'position': u'5662'},
u'cds': {u'length': u'5592', u'position': u'5430'},
u'effect': u'synonymous_variant',
u'feature_id': u'NM_007294.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5430G>A',
u'hgvs_p': u'p.Val1810Val',
u'protein': {u'length': u'1863', u'position': u'1810'},
u'putative_impact': u'LOW',
u'rank': u'22',
u'total': u'23',
u'transcript_biotype': u'Coding'},
{u'effect': u'non_coding_exon_variant',
u'feature_id': u'NR_027676.1',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'n.5566G>A',
u'putative_impact': u'MODIFIER',
u'rank': u'22',
u'total': u'23',
u'transcript_biotype': u'Noncoding'}]},
u'vcf': {u'alt': u'T', u'position': u'41199697', u'ref': u'C'}},
{u'_id': u'chr17:g.41199697_41199702del',
u'_score': 12.69064,
u'clinvar': {u'allele_id': 70241,
u'alt': u'-',
u'chrom': u'17',
u'cytogenic': u'17q21.31',
u'gene': {u'id': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41199702, u'start': 41199697},
u'hg38': {u'end': 43047685, u'start': 43047680},
u'hgvs': {u'coding': [u'LRG_292t1:c.5425_5430delGTTGTG',
u'NM_007294.3:c.5425_5430delGTTGTG'],
u'genomic': [u'LRG_292:g.170299_170304delGTTGTG',
u'NG_005905.2:g.170299_170304delGTTGTG',
u'NC_000017.11:g.43047680_43047685delCACAAC',
u'NC_000017.10:g.41199697_41199702delCACAAC']},
u'rcv': [{u'accession': u'RCV000048989',
u'clinical_significance': u'not provided',
u'conditions': {u'identifiers': {u'medgen': u'C0346153',
u'omim': u'114480'},
u'name': u'Familial cancer of breast',
u'synonyms': [u'CHEK2-Related Breast Cancer',
u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer']},
u'last_evaluated': u'2013-02-01',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5425_5430delGTTGTG (p.Val1809_Val1810del)',
u'review_status': u'no assertion provided'},
{u'accession': u'RCV000112652',
u'clinical_significance': u'Uncertain significance',
u'conditions': {u'age_of_onset': u'All ages',
u'identifiers': {u'medgen': u'C2676676',
u'omim': u'604370',
u'orphanet': u'145'},
u'name': u'Breast-ovarian cancer, familial 1 (BROVCA1)',
u'synonyms': [u'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'OVARIAN CANCER, SUSCEPTIBILITY TO',
u'BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'Breast cancer, familial 1',
u'hereditary breast and ovarian cancer, BROVCA1',
u'Breast-ovarian cancer, familial, 1']},
u'last_evaluated': u'1999-04-06',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5425_5430delGTTGTG (p.Val1809_Val1810del)',
u'review_status': u'no assertion criteria provided'}],
u'ref': u'CACAAC',
u'rsid': u'rs80358348',
u'type': u'Deletion',
u'variant_id': 55574},
u'dbsnp': {u'allele_origin': u'unspecified',
u'alleles': [{u'allele': u'GCACAAC'}, {u'allele': u'G'}],
u'alt': u'G',
u'chrom': u'17',
u'class': u'DIV',
u'dbsnp_build': 132,
u'flags': [u'ASP', u'LSD', u'PM', u'RV', u'SLO'],
u'gene': {u'geneid': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41199702, u'start': 41199697},
u'ref': u'GCACAAC',
u'rsid': u'rs80358348',
u'validated': False,
u'var_subtype': u'del',
u'vartype': u'indel'},
u'snpeff': {u'ann': [{u'cdna': {u'length': u'7270', u'position': u'5725'},
u'cds': {u'length': u'5655', u'position': u'5488'},
u'effect': u'inframe_deletion',
u'feature_id': u'NM_007300.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5488_5493delGTTGTG',
u'hgvs_p': u'p.Val1830_Val1831del',
u'protein': {u'length': u'1884', u'position': u'1830'},
u'putative_impact': u'MODERATE',
u'rank': u'23',
u'total': u'24',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'3682', u'position': u'2137'},
u'cds': {u'length': u'2280', u'position': u'2113'},
u'effect': u'inframe_deletion',
u'feature_id': u'NM_007298.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.2113_2118delGTTGTG',
u'hgvs_p': u'p.Val705_Val706del',
u'protein': {u'length': u'759', u'position': u'705'},
u'putative_impact': u'MODERATE',
u'rank': u'21',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'7115', u'position': u'5570'},
u'cds': {u'length': u'5451', u'position': u'5284'},
u'effect': u'inframe_deletion',
u'feature_id': u'NM_007297.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5284_5289delGTTGTG',
u'hgvs_p': u'p.Val1762_Val1763del',
u'protein': {u'length': u'1816', u'position': u'1762'},
u'putative_impact': u'MODERATE',
u'rank': u'21',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'7207', u'position': u'5662'},
u'cds': {u'length': u'5592', u'position': u'5425'},
u'effect': u'inframe_deletion',
u'feature_id': u'NM_007294.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5425_5430delGTTGTG',
u'hgvs_p': u'p.Val1809_Val1810del',
u'protein': {u'length': u'1863', u'position': u'1809'},
u'putative_impact': u'MODERATE',
u'rank': u'22',
u'total': u'23',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'3783', u'position': u'2238'},
u'cds': {u'length': u'2100', u'position': u'2039'},
u'effect': u'disruptive_inframe_deletion',
u'feature_id': u'NM_007299.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.2039_2044delGTTGTG',
u'hgvs_p': u'p.Gly680_Cys681del',
u'protein': {u'length': u'699', u'position': u'680'},
u'putative_impact': u'MODERATE',
u'rank': u'21',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'effect': u'non_coding_exon_variant',
u'feature_id': u'NR_027676.1',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'n.5561_5566delGTTGTG',
u'putative_impact': u'MODIFIER',
u'rank': u'22',
u'total': u'23',
u'transcript_biotype': u'Noncoding'}]},
u'vcf': {u'alt': u'G', u'position': u'41199696', u'ref': u'GCACAAC'}},
{u'_id': u'chr17:g.41199702C>A',
u'_score': 12.69064,
u'cadd': {u'_license': u'http://goo.gl/bkpNhq',
u'alt': u'A',
u'anc': u'C',
u'annotype': u'CodingTranscript',
u'bstatistic': 116,
u'chmm': {u'bivflnk': 0.0,
u'enh': 0.0,
u'enhbiv': 0.0,
u'het': 0.0,
u'quies': 0.276,
u'reprpc': 0.0,
u'reprpcwk': 0.0,
u'tssa': 0.0,
u'tssaflnk': 0.0,
u'tssbiv': 0.0,
u'tx': 0.213,
u'txflnk': 0.0,
u'txwk': 0.512,
u'znfrpts': 0.0},
u'chrom': 17,
u'consdetail': u'missense',
u'consequence': u'NON_SYNONYMOUS',
u'consscore': 7,
u'cpg': 0.0,
u'dna': {u'helt': 0.87, u'mgw': -0.33, u'prot': -5.48, u'roll': -1.99},
u'dst2splice': 19,
u'dst2spltype': u'ACCEPTOR',
u'encode': {u'exp': 244.65,
u'h3k27ac': 5.0,
u'h3k4me1': 3.0,
u'h3k4me3': 6.0,
u'nucleo': 2.4},
u'exon': u'23/24',
u'fitcons': 0.701516,
u'gc': 0.52,
u'gene': {u'ccds_id': u'CCDS11456.2',
u'cds': {u'cdna_pos': 5720,
u'cds_pos': 5488,
u'rel_cdna_pos': 0.96,
u'rel_cds_pos': 0.97},
u'feature_id': u'ENST00000471181',
u'gene_id': u'ENSG00000012048',
u'genename': u'BRCA1',
u'prot': {u'domain': u'ndomain',
u'protpos': 1830,
u'rel_prot_pos': 0.97}},
u'gerp': {u'n': 4.98, u'rs': 137.8, u'rs_pval': 2.45126e-14, u's': 2.97},
u'grantham': 50,
u'isderived': u'TRUE',
u'isknownvariant': u'FALSE',
u'istv': u'TRUE',
u'length': 0,
u'mapability': {u'20bp': 1, u'35bp': 1},
u'min_dist_tse': 2007,
u'min_dist_tss': 76431,
u'mutindex': 32,
u'naa': u'F',
u'oaa': u'V',
u'phast_cons': {u'mammalian': 0.983,
u'primate': 0.882,
u'vertebrate': 0.991},
u'phred': 32,
u'phylop': {u'mammalian': 0.675, u'primate': 0.457, u'vertebrate': 0.903},
u'polyphen': {u'cat': u'probably_damaging', u'val': 0.97},
u'pos': 41199702,
u'rawscore': 6.745557,
u'ref': u'C',
u'segway': u'GE1',
u'sift': {u'cat': u'deleterious', u'val': 0},
u'type': u'SNV'},
u'clinvar': {u'allele_id': 70240,
u'alt': u'A',
u'chrom': u'17',
u'cytogenic': u'17q21.31',
u'gene': {u'id': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41199702, u'start': 41199702},
u'hg38': {u'end': 43047685, u'start': 43047685},
u'hgvs': {u'coding': [u'LRG_292t1:c.5425G>T', u'NM_007294.3:c.5425G>T'],
u'genomic': [u'LRG_292:g.170299G>T',
u'NG_005905.2:g.170299G>T',
u'NC_000017.11:g.43047685C>A',
u'NC_000017.10:g.41199702C>A']},
u'rcv': [{u'accession': u'RCV000048988',
u'clinical_significance': u'not provided',
u'conditions': {u'identifiers': {u'medgen': u'C0346153',
u'omim': u'114480'},
u'name': u'Familial cancer of breast',
u'synonyms': [u'CHEK2-Related Breast Cancer',
u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer']},
u'last_evaluated': u'2013-02-01',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5425G>T (p.Val1809Phe)',
u'review_status': u'no assertion provided'},
{u'accession': u'RCV000112651',
u'clinical_significance': u'Uncertain significance',
u'conditions': {u'age_of_onset': u'All ages',
u'identifiers': {u'medgen': u'C2676676',
u'omim': u'604370',
u'orphanet': u'145'},
u'name': u'Breast-ovarian cancer, familial 1 (BROVCA1)',
u'synonyms': [u'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'OVARIAN CANCER, SUSCEPTIBILITY TO',
u'BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'Breast cancer, familial 1',
u'hereditary breast and ovarian cancer, BROVCA1',
u'Breast-ovarian cancer, familial, 1']},
u'last_evaluated': u'2002-05-29',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5425G>T (p.Val1809Phe)',
u'review_status': u'no assertion criteria provided'}],
u'ref': u'C',
u'rsid': u'rs28897698',
u'type': u'single nucleotide variant',
u'variant_id': 55573},
u'dbnsfp': {u'aa': [{u'alt': u'V',
u'codonpos': 2,
u'pos': 680,
u'ref': u'G',
u'refcodon': u'GGT'},
{u'alt': u'F',
u'codonpos': 1,
u'pos': [u'1809',
u'667',
u'119',
u'300',
u'42',
u'1762',
u'1830',
u'705'],
u'ref': u'V',
u'refcodon': u'GTT'}],
u'alt': u'A',
u'ancestral_allele': u'C',
u'cds_strand': u'-',
u'chrom': u'17',
u'ensembl': {u'geneid': u'ENSG00000012048',
u'proteinid': u'ENSP00000417148',
u'transcriptid': u'ENST00000468300'},
u'fathmm': {u'pred': u'D', u'rankscore': 0.87685, u'score': -2.3},
u'fathmm-mkl': {u'coding_group': u'AEFBI',
u'coding_pred': u'D',
u'coding_rankscore': 0.32918,
u'coding_score': 0.66752},
u'genename': u'BRCA1',
u'gerp++': {u'nr': 4.98, u'rs': 2.97, u'rs_rankscore': 0.33223},
u'gm12878': {u'confidence_value': 0,
u'fitcons_rankscore': 0.89268,
u'fitcons_score': 0.724815},
u'h1-hesc': {u'confidence_value': 0,
u'fitcons_rankscore': 0.87815,
u'fitcons_score': 0.724815},
u'hg18': {u'end': 38453228, u'start': 38453228},
u'hg19': {u'end': 41199702, u'start': 41199702},
u'hg38': {u'end': 43047685, u'start': 43047685},
u'huvec': {u'confidence_value': 0,
u'fitcons_rankscore': 0.83205,
u'fitcons_score': 0.714379},
u'integrated': {u'confidence_value': 0,
u'fitcons_rankscore': 0.72903,
u'fitcons_score': 0.706548},
u'metalr': {u'pred': u'D', u'rankscore': 0.93339, u'score': 0.803},
u'metasvm': {u'pred': u'D', u'rankscore': 0.86381, u'score': 0.2276},
u'mutationtaster': {u'AAE': [u'G680V',
u'V1809F',
u'V119F',
u'V300F',
u'V42F',
u'V1762F',
u'V1830F',
u'V705F',
u'V1544F',
u'V667F',
u'V1570F',
u'V626F',
u'V658F',
u'V1513F'],
u'converted_rankscore': 0.39483,
u'model': [u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae'],
u'pred': [u'D',
u'N',
u'N',
u'N',
u'N',
u'N',
u'N',
u'N',
u'N',
u'N',
u'N',
u'N',
u'N',
u'N'],
u'score': [0.978687,
0.64294,
0.574257,
0.574257,
0.713266,
0.617361,
0.64294,
0.574257,
0.995933,
0.574257,
0.995933,
0.574257,
0.574257,
0.931237]},
u'phastcons': {u'20way': {u'mammalian': 0.615,
u'mammalian_rankscore': 0.2897},
u'7way': {u'vertebrate': 0.244, u'vertebrate_rankscore': 0.21102}},
u'phylo': {u'p20way': {u'mammalian': 0.022,
u'mammalian_rankscore': 0.14435},
u'p7way': {u'vertebrate': -0.621, u'vertebrate_rankscore': 0.03621}},
u'polyphen2': {u'hdiv': {u'pred': u'P',
u'rankscore': 0.50293,
u'score': 0.935},
u'hvar': {u'pred': u'P', u'rankscore': 0.45284, u'score': 0.481}},
u'provean': {u'pred': u'N', u'rankscore': 0.0336, u'score': 0.42},
u'ref': u'C',
u'reliability_index': 9,
u'rsid': u'rs28897698',
u'sift': {u'converted_rankscore': 0.91219, u'pred': u'D', u'score': 0.0},
u'siphy_29way': {u'logodds': 6.5492,
u'logodds_rankscore': 0.21406,
u'pi': {u'a': 0.0, u'c': 0.7208, u'g': 0.1826, u't': 0.0966}},
u'uniprot': {u'acc': u'Q6IN79', u'pos': u'680'}},
u'dbsnp': {u'allele_origin': u'unspecified',
u'alleles': [{u'allele': u'C'}, {u'allele': u'A'}],
u'alt': u'A',
u'chrom': u'17',
u'class': u'SNV',
u'dbsnp_build': 125,
u'flags': [u'ASP',
u'HD',
u'LSD',
u'NSM',
u'PM',
u'REF',
u'RV',
u'S3D',
u'SLO'],
u'gene': {u'geneid': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41199703, u'start': 41199702},
u'ref': u'C',
u'rsid': u'rs28897698',
u'validated': False,
u'var_subtype': u'tv',
u'vartype': u'snp'},
u'mutdb': {u'alt': u'T',
u'chrom': u'17',
u'hg19': {u'end': 41199702, u'start': 41199702},
u'mutpred_score': 0.797,
u'ref': u'G',
u'rsid': u'rs28897698',
u'strand': u'm'},
u'snpeff': {u'ann': [{u'cdna': {u'length': u'7270', u'position': u'5720'},
u'cds': {u'length': u'5655', u'position': u'5488'},
u'effect': u'missense_variant',
u'feature_id': u'NM_007300.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5488G>T',
u'hgvs_p': u'p.Val1830Phe',
u'protein': {u'length': u'1884', u'position': u'1830'},
u'putative_impact': u'MODERATE',
u'rank': u'23',
u'total': u'24',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'3682', u'position': u'2132'},
u'cds': {u'length': u'2280', u'position': u'2113'},
u'effect': u'missense_variant',
u'feature_id': u'NM_007298.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.2113G>T',
u'hgvs_p': u'p.Val705Phe',
u'protein': {u'length': u'759', u'position': u'705'},
u'putative_impact': u'MODERATE',
u'rank': u'21',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'7115', u'position': u'5565'},
u'cds': {u'length': u'5451', u'position': u'5284'},
u'effect': u'missense_variant',
u'feature_id': u'NM_007297.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5284G>T',
u'hgvs_p': u'p.Val1762Phe',
u'protein': {u'length': u'1816', u'position': u'1762'},
u'putative_impact': u'MODERATE',
u'rank': u'21',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'3783', u'position': u'2233'},
u'cds': {u'length': u'2100', u'position': u'2039'},
u'effect': u'missense_variant',
u'feature_id': u'NM_007299.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.2039G>T',
u'hgvs_p': u'p.Gly680Val',
u'protein': {u'length': u'699', u'position': u'680'},
u'putative_impact': u'MODERATE',
u'rank': u'21',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'7207', u'position': u'5657'},
u'cds': {u'length': u'5592', u'position': u'5425'},
u'effect': u'missense_variant',
u'feature_id': u'NM_007294.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5425G>T',
u'hgvs_p': u'p.Val1809Phe',
u'protein': {u'length': u'1863', u'position': u'1809'},
u'putative_impact': u'MODERATE',
u'rank': u'22',
u'total': u'23',
u'transcript_biotype': u'Coding'},
{u'effect': u'non_coding_exon_variant',
u'feature_id': u'NR_027676.1',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'n.5561G>T',
u'putative_impact': u'MODIFIER',
u'rank': u'22',
u'total': u'23',
u'transcript_biotype': u'Noncoding'}]},
u'vcf': {u'alt': u'A', u'position': u'41199702', u'ref': u'C'}}],
u'max_score': 12.69064,
u'took': 17,
u'total': 3532}
mv.query('clinvar.gene.symbol:BRCA1', size=5)
{u'hits': [{u'_id': u'NM_007294.3:c.4358-?_5277+?del',
u'_score': 12.69064,
u'clinvar': {u'allele_id': 94606,
u'chrom': u'17',
u'coding_hgvs_only': True,
u'cytogenic': u'17q21.31',
u'gene': {u'id': u'672', u'symbol': u'BRCA1'},
u'hgvs': {u'coding': [u'LRG_292t1:c.4358-?_5277+?del',
u'NM_007294.3:c.4358-?_5277+?del'],
u'genomic': [u'LRG_292:g.(?_141370_160932_?)del',
u'NC_000017.11:g.(?_43057052)_(43076614_?)del',
u'NC_000017.10:g.(?_41209069)_(41228631_?)del']},
u'rcv': [{u'accession': u'RCV000119187',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'identifiers': {u'medgen': u'C0677776'},
u'name': u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer (HBOC)',
u'synonyms': [u'q', u'Hereditary breast and ovarian cancer syndrome']},
u'last_evaluated': u'2014-03-27',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.4358-?_5277+?del',
u'review_status': u'no assertion criteria provided'},
{u'accession': u'RCV000074593',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'identifiers': {u'medgen': u'C0346153',
u'omim': u'114480'},
u'name': u'Familial cancer of breast',
u'synonyms': [u'CHEK2-Related Breast Cancer',
u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer']},
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.4358-?_5277+?del',
u'review_status': u'criteria provided, single submitter'}],
u'type': u'Deletion',
u'variant_id': 89063}},
{u'_id': u'chr17:g.41197590_41197593del',
u'_score': 12.69064,
u'clinvar': {u'allele_id': 102794,
u'alt': u'-',
u'chrom': u'17',
u'cytogenic': u'17q21.31',
u'gene': {u'id': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41197593, u'start': 41197590},
u'hg38': {u'end': 43045576, u'start': 43045573},
u'hgvs': {u'coding': [u'LRG_292t1:c.*102_*105delCTGT',
u'NM_007294.3:c.*102_*105delCTGT'],
u'genomic': [u'LRG_292:g.172408_172411delCTGT',
u'NG_005905.2:g.172408_172411delCTGT',
u'NC_000017.11:g.43045573_43045576delACAG',
u'NC_000017.10:g.41197590_41197593delACAG']},
u'rcv': {u'accession': u'RCV000083012',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'age_of_onset': u'All ages',
u'identifiers': {u'medgen': u'C2676676',
u'omim': u'604370',
u'orphanet': u'145'},
u'name': u'Breast-ovarian cancer, familial 1 (BROVCA1)',
u'synonyms': [u'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'OVARIAN CANCER, SUSCEPTIBILITY TO',
u'BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'Breast cancer, familial 1',
u'hereditary breast and ovarian cancer, BROVCA1',
u'Breast-ovarian cancer, familial, 1']},
u'last_evaluated': u'2011-10-17',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.*102_*105delCTGT',
u'review_status': u'no assertion criteria provided'},
u'ref': u'ACAG',
u'rsid': u'rs431825382',
u'type': u'Deletion',
u'variant_id': 96891},
u'snpeff': {u'ann': [{u'distance_to_feature': u'102',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007300.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*102_*105delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'24',
u'total': u'24',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'102',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007298.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*102_*105delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'102',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007297.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*102_*105delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'208',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007299.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*208_*211delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'102',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007294.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*102_*105delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'23',
u'total': u'23',
u'transcript_biotype': u'Coding'},
{u'effect': u'non_coding_exon_variant',
u'feature_id': u'NR_027676.1',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'n.5830_5833delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'23',
u'total': u'23',
u'transcript_biotype': u'Noncoding'}]},
u'vcf': {u'alt': u'G', u'position': u'41197589', u'ref': u'GACAG'}},
{u'_id': u'chr17:g.41197737C>G',
u'_score': 12.69064,
u'cadd': {u'_license': u'http://goo.gl/bkpNhq',
u'alt': u'G',
u'anc': u'C',
u'annotype': u'CodingTranscript',
u'bstatistic': 116,
u'chmm': {u'bivflnk': 0.0,
u'enh': 0.008,
u'enhbiv': 0.0,
u'het': 0.0,
u'quies': 0.299,
u'reprpc': 0.0,
u'reprpcwk': 0.0,
u'tssa': 0.0,
u'tssaflnk': 0.0,
u'tssbiv': 0.0,
u'tx': 0.205,
u'txflnk': 0.0,
u'txwk': 0.48,
u'znfrpts': 0.0},
u'chrom': 17,
u'consdetail': u'synonymous',
u'consequence': u'SYNONYMOUS',
u'consscore': 5,
u'cpg': 0.01,
u'dna': {u'helt': 1.78, u'mgw': 0.48, u'prot': -0.7, u'roll': -0.17},
u'encode': {u'exp': 371.32,
u'h3k27ac': 12.76,
u'h3k4me1': 3.0,
u'h3k4me3': 3.0,
u'nucleo': 1.3},
u'exon': u'24/24',
u'fitcons': 0.723164,
u'gc': 0.6,
u'gene': {u'ccds_id': u'CCDS11456.2',
u'cds': {u'cdna_pos': 5845,
u'cds_pos': 5613,
u'rel_cdna_pos': 0.98,
u'rel_cds_pos': 0.99},
u'feature_id': u'ENST00000471181',
u'gene_id': u'ENSG00000012048',
u'genename': u'BRCA1',
u'prot': {u'domain': u'ndomain',
u'protpos': 1871,
u'rel_prot_pos': 0.99}},
u'gerp': {u'n': 5.32, u'rs': 844.9, u'rs_pval': 8.78912e-51, u's': 4.33},
u'isderived': u'TRUE',
u'isknownvariant': u'FALSE',
u'istv': u'TRUE',
u'length': 0,
u'mapability': {u'20bp': 0.5, u'35bp': 1},
u'min_dist_tse': 42,
u'min_dist_tss': 78396,
u'mirsvr': {u'aln': 148, u'e': -24.01, u'score': -0.2148},
u'mutindex': 8,
u'naa': u'L',
u'oaa': u'L',
u'phast_cons': {u'mammalian': 1.0, u'primate': 0.997, u'vertebrate': 1.0},
u'phred': 12.85,
u'phylop': {u'mammalian': 2.766, u'primate': 0.559, u'vertebrate': 1.674},
u'pos': 41197737,
u'rawscore': 1.4117,
u'ref': u'C',
u'segway': u'TF2',
u'type': u'SNV'},
u'clinvar': {u'allele_id': 184867,
u'alt': u'G',
u'chrom': u'17',
u'cytogenic': u'17q21.31',
u'gene': {u'id': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41197737, u'start': 41197737},
u'hg38': {u'end': 43045720, u'start': 43045720},
u'hgvs': {u'coding': [u'LRG_292t1:c.5550G>C',
u'NM_007299.3:c.*64G>C',
u'NM_007294.3:c.5550G>C'],
u'genomic': [u'LRG_292:g.172264G>C',
u'NG_005905.2:g.172264G>C',
u'NC_000017.11:g.43045720C>G',
u'NC_000017.10:g.41197737C>G']},
u'rcv': {u'accession': u'RCV000163767',
u'clinical_significance': u'Likely benign',
u'conditions': {u'identifiers': {u'medgen': u'C0027672'},
u'name': u'Hereditary cancer-predisposing syndrome',
u'synonyms': u'Neoplastic Syndromes, Hereditary'},
u'last_evaluated': u'2013-12-19',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5550G>C (p.Leu1850=)',
u'review_status': u'criteria provided, single submitter'},
u'ref': u'C',
u'rsid': u'rs786201502',
u'type': u'single nucleotide variant',
u'variant_id': 184500},
u'snpeff': {u'ann': [{u'cdna': {u'length': u'7270', u'position': u'5845'},
u'cds': {u'length': u'5655', u'position': u'5613'},
u'effect': u'synonymous_variant',
u'feature_id': u'NM_007300.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5613G>C',
u'hgvs_p': u'p.Leu1871Leu',
u'protein': {u'length': u'1884', u'position': u'1871'},
u'putative_impact': u'LOW',
u'rank': u'24',
u'total': u'24',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'3682', u'position': u'2257'},
u'cds': {u'length': u'2280', u'position': u'2238'},
u'effect': u'synonymous_variant',
u'feature_id': u'NM_007298.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.2238G>C',
u'hgvs_p': u'p.Leu746Leu',
u'protein': {u'length': u'759', u'position': u'746'},
u'putative_impact': u'LOW',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'7115', u'position': u'5690'},
u'cds': {u'length': u'5451', u'position': u'5409'},
u'effect': u'synonymous_variant',
u'feature_id': u'NM_007297.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5409G>C',
u'hgvs_p': u'p.Leu1803Leu',
u'protein': {u'length': u'1816', u'position': u'1803'},
u'putative_impact': u'LOW',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'7207', u'position': u'5782'},
u'cds': {u'length': u'5592', u'position': u'5550'},
u'effect': u'synonymous_variant',
u'feature_id': u'NM_007294.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5550G>C',
u'hgvs_p': u'p.Leu1850Leu',
u'protein': {u'length': u'1863', u'position': u'1850'},
u'putative_impact': u'LOW',
u'rank': u'23',
u'total': u'23',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'64',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007299.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*64G>C',
u'putative_impact': u'MODIFIER',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'effect': u'non_coding_exon_variant',
u'feature_id': u'NR_027676.1',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'n.5686G>C',
u'putative_impact': u'MODIFIER',
u'rank': u'23',
u'total': u'23',
u'transcript_biotype': u'Noncoding'}]},
u'vcf': {u'alt': u'G', u'position': u'41197737', u'ref': u'C'}},
{u'_id': u'chr17:g.41197776C>T',
u'_score': 12.69064,
u'cadd': {u'_license': u'http://goo.gl/bkpNhq',
u'alt': u'T',
u'anc': u'C',
u'annotype': u'CodingTranscript',
u'bstatistic': 116,
u'chmm': {u'bivflnk': 0.0,
u'enh': 0.008,
u'enhbiv': 0.0,
u'het': 0.0,
u'quies': 0.299,
u'reprpc': 0.0,
u'reprpcwk': 0.0,
u'tssa': 0.0,
u'tssaflnk': 0.0,
u'tssbiv': 0.0,
u'tx': 0.205,
u'txflnk': 0.0,
u'txwk': 0.48,
u'znfrpts': 0.0},
u'chrom': 17,
u'consdetail': u'stop_gained',
u'consequence': u'STOP_GAINED',
u'consscore': 8,
u'cpg': 0.01,
u'dna': {u'helt': 1.68, u'mgw': 0.28, u'prot': -2.32, u'roll': 0.2},
u'encode': {u'exp': 383.33,
u'h3k27ac': 11.52,
u'h3k4me1': 4.0,
u'h3k4me3': 2.56,
u'nucleo': 3.3},
u'exon': u'24/24',
u'fitcons': 0.723164,
u'gc': 0.56,
u'gene': {u'ccds_id': u'CCDS11456.2',
u'cds': {u'cdna_pos': 5806,
u'cds_pos': 5574,
u'rel_cdna_pos': 0.98,
u'rel_cds_pos': 0.99},
u'feature_id': u'ENST00000471181',
u'gene_id': u'ENSG00000012048',
u'genename': u'BRCA1',
u'prot': {u'domain': u'ndomain',
u'protpos': 1858,
u'rel_prot_pos': 0.99}},
u'gerp': {u'n': 5.32, u'rs': 844.9, u'rs_pval': 8.78912e-51, u's': 5.32},
u'isderived': u'TRUE',
u'isknownvariant': u'FALSE',
u'istv': u'FALSE',
u'length': 0,
u'mapability': {u'20bp': 1, u'35bp': 1},
u'min_dist_tse': 81,
u'min_dist_tss': 78357,
u'mirsvr': {u'aln': 127, u'e': -21.58, u'score': -0.1772},
u'mutindex': 41,
u'naa': u'*',
u'oaa': u'W',
u'phast_cons': {u'mammalian': 1.0, u'primate': 0.997, u'vertebrate': 1.0},
u'phred': 49,
u'phylop': {u'mammalian': 2.766, u'primate': 0.559, u'vertebrate': 3.085},
u'pos': 41197776,
u'rawscore': 15.183713,
u'ref': u'C',
u'segway': u'TF2',
u'type': u'SNV'},
u'clinvar': {u'allele_id': 70276,
u'alt': u'T',
u'chrom': u'17',
u'cytogenic': u'17q21.31',
u'gene': {u'id': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41197776, u'start': 41197776},
u'hg38': {u'end': 43045759, u'start': 43045759},
u'hgvs': {u'coding': [u'LRG_292t1:c.5511G>A',
u'NM_007299.3:c.*25G>A',
u'NM_007294.3:c.5511G>A'],
u'genomic': [u'LRG_292:g.172225G>A',
u'NG_005905.2:g.172225G>A',
u'NC_000017.11:g.43045759C>T',
u'NC_000017.10:g.41197776C>T']},
u'rcv': [{u'accession': u'RCV000049029',
u'clinical_significance': u'not provided',
u'conditions': {u'identifiers': {u'medgen': u'C0346153',
u'omim': u'114480'},
u'name': u'Familial cancer of breast',
u'synonyms': [u'CHEK2-Related Breast Cancer',
u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer']},
u'last_evaluated': u'2013-02-01',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5511G>A (p.Trp1837Ter)',
u'review_status': u'no assertion provided'},
{u'accession': u'RCV000112692',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'age_of_onset': u'All ages',
u'identifiers': {u'medgen': u'C2676676',
u'omim': u'604370',
u'orphanet': u'145'},
u'name': u'Breast-ovarian cancer, familial 1 (BROVCA1)',
u'synonyms': [u'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'OVARIAN CANCER, SUSCEPTIBILITY TO',
u'BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'Breast cancer, familial 1',
u'hereditary breast and ovarian cancer, BROVCA1',
u'Breast-ovarian cancer, familial, 1']},
u'last_evaluated': u'2006-07-19',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5511G>A (p.Trp1837Ter)',
u'review_status': u'no assertion criteria provided'}],
u'ref': u'C',
u'rsid': u'rs80356914',
u'type': u'single nucleotide variant',
u'variant_id': 55609},
u'dbnsfp': {u'aa': {u'alt': u'X',
u'codonpos': 3,
u'pos': [u'1837',
u'695',
u'147',
u'328',
u'70',
u'1790',
u'1858',
u'733'],
u'ref': u'W',
u'refcodon': u'TGG'},
u'alt': u'T',
u'ancestral_allele': u'C',
u'cds_strand': u'-',
u'chrom': u'17',
u'clinvar': {u'clinsig': 5,
u'rs': u'rs80356914',
u'trait': u'Breast-ovarian_cancer\\x2c_familial_1'},
u'ensembl': {u'geneid': u'ENSG00000012048',
u'proteinid': [u'ENSP00000350283',
u'ENSP00000312236',
u'ENSP00000465818',
u'ENSP00000467329',
u'ENSP00000465347',
u'ENSP00000418775',
u'ENSP00000418960',
u'ENSP00000420705'],
u'transcriptid': [u'ENST00000357654',
u'ENST00000352993',
u'ENST00000586385',
u'ENST00000591534',
u'ENST00000591849',
u'ENST00000493795',
u'ENST00000471181',
u'ENST00000491747']},
u'fathmm-mkl': {u'coding_group': u'AEFBI',
u'coding_pred': u'D',
u'coding_rankscore': 0.52871,
u'coding_score': 0.91246},
u'genename': u'BRCA1',
u'gerp++': {u'nr': 5.32, u'rs': 5.32, u'rs_rankscore': 0.75224},
u'gm12878': {u'confidence_value': 0,
u'fitcons_rankscore': 0.89268,
u'fitcons_score': 0.724815},
u'h1-hesc': {u'confidence_value': 0,
u'fitcons_rankscore': 0.96044,
u'fitcons_score': 0.743671},
u'hg18': {u'end': 38451302, u'start': 38451302},
u'hg19': {u'end': 41197776, u'start': 41197776},
u'hg38': {u'end': 43045759, u'start': 43045759},
u'huvec': {u'confidence_value': 0,
u'fitcons_rankscore': 0.83205,
u'fitcons_score': 0.714379},
u'integrated': {u'confidence_value': 0,
u'fitcons_rankscore': 0.92359,
u'fitcons_score': 0.732398},
u'interpro_domain': u'BRCT domain',
u'lrt': {u'converted_rankscore': 0.49118,
u'omega': 0.0,
u'pred': u'D',
u'score': 0.000149},
u'mutationtaster': {u'AAE': [u'W695*',
u'W1598*',
u'W654*',
u'W686*',
u'W1541*',
u'W1837*',
u'W147*',
u'W328*',
u'W70*',
u'W1790*',
u'W1858*',
u'W733*',
u'W1572*',
u'.'],
u'converted_rankscore': 0.81033,
u'model': [u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'without_aae'],
u'pred': [u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'D'],
u'score': [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]},
u'phastcons': {u'20way': {u'mammalian': 0.994,
u'mammalian_rankscore': 0.58582},
u'7way': {u'vertebrate': 0.997, u'vertebrate_rankscore': 0.67089}},
u'phylo': {u'p20way': {u'mammalian': 0.935,
u'mammalian_rankscore': 0.48811},
u'p7way': {u'vertebrate': 0.871, u'vertebrate_rankscore': 0.44667}},
u'ref': u'C',
u'rsid': u'rs80356914',
u'siphy_29way': {u'logodds': 14.3724,
u'logodds_rankscore': 0.66207,
u'pi': {u'a': 0.0, u'c': 1.0, u'g': 0.0, u't': 0.0}}},
u'dbsnp': {u'allele_origin': u'unspecified',
u'alleles': [{u'allele': u'C'}, {u'allele': u'A'}, {u'allele': u'T'}],
u'alt': u'T',
u'chrom': u'17',
u'class': u'SNV',
u'dbsnp_build': 132,
u'flags': [u'ASP',
u'LSD',
u'NSM',
u'NSN',
u'PM',
u'REF',
u'RV',
u'S3D',
u'SLO',
u'U3'],
u'gene': {u'geneid': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41197777, u'start': 41197776},
u'ref': u'C',
u'rsid': u'rs80356914',
u'validated': False,
u'var_subtype': u'unknown',
u'vartype': u'snp'},
u'snpeff': {u'ann': [{u'cdna': {u'length': u'7270', u'position': u'5806'},
u'cds': {u'length': u'5655', u'position': u'5574'},
u'effect': u'stop_gained',
u'feature_id': u'NM_007300.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5574G>A',
u'hgvs_p': u'p.Trp1858*',
u'protein': {u'length': u'1884', u'position': u'1858'},
u'putative_impact': u'HIGH',
u'rank': u'24',
u'total': u'24',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'3682', u'position': u'2218'},
u'cds': {u'length': u'2280', u'position': u'2199'},
u'effect': u'stop_gained',
u'feature_id': u'NM_007298.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.2199G>A',
u'hgvs_p': u'p.Trp733*',
u'protein': {u'length': u'759', u'position': u'733'},
u'putative_impact': u'HIGH',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'7115', u'position': u'5651'},
u'cds': {u'length': u'5451', u'position': u'5370'},
u'effect': u'stop_gained',
u'feature_id': u'NM_007297.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5370G>A',
u'hgvs_p': u'p.Trp1790*',
u'protein': {u'length': u'1816', u'position': u'1790'},
u'putative_impact': u'HIGH',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'7207', u'position': u'5743'},
u'cds': {u'length': u'5592', u'position': u'5511'},
u'effect': u'stop_gained',
u'feature_id': u'NM_007294.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5511G>A',
u'hgvs_p': u'p.Trp1837*',
u'protein': {u'length': u'1863', u'position': u'1837'},
u'putative_impact': u'HIGH',
u'rank': u'23',
u'total': u'23',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'25',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007299.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*25G>A',
u'putative_impact': u'MODIFIER',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'effect': u'non_coding_exon_variant',
u'feature_id': u'NR_027676.1',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'n.5647G>A',
u'putative_impact': u'MODIFIER',
u'rank': u'23',
u'total': u'23',
u'transcript_biotype': u'Noncoding'}]},
u'vcf': {u'alt': u'T', u'position': u'41197776', u'ref': u'C'}},
{u'_id': u'chr17:g.41197790C>T',
u'_score': 12.69064,
u'cadd': {u'_license': u'http://goo.gl/bkpNhq',
u'alt': u'T',
u'anc': u'C',
u'annotype': u'CodingTranscript',
u'bstatistic': 116,
u'chmm': {u'bivflnk': 0.0,
u'enh': 0.008,
u'enhbiv': 0.0,
u'het': 0.0,
u'quies': 0.299,
u'reprpc': 0.0,
u'reprpcwk': 0.0,
u'tssa': 0.0,
u'tssaflnk': 0.0,
u'tssbiv': 0.0,
u'tx': 0.205,
u'txflnk': 0.0,
u'txwk': 0.48,
u'znfrpts': 0.0},
u'chrom': 17,
u'consdetail': u'missense',
u'consequence': u'NON_SYNONYMOUS',
u'consscore': 7,
u'cpg': 0.01,
u'dna': {u'helt': 2.28, u'mgw': 0.13, u'prot': -3.43, u'roll': 0.29},
u'encode': {u'exp': 327.44,
u'h3k27ac': 11.52,
u'h3k4me1': 4.0,
u'h3k4me3': 2.56,
u'nucleo': 4.2},
u'exon': u'24/24',
u'fitcons': 0.723164,
u'gc': 0.53,
u'gene': {u'ccds_id': u'CCDS11456.2',
u'cds': {u'cdna_pos': 5792,
u'cds_pos': 5560,
u'rel_cdna_pos': 0.98,
u'rel_cds_pos': 0.98},
u'feature_id': u'ENST00000471181',
u'gene_id': u'ENSG00000012048',
u'genename': u'BRCA1',
u'prot': {u'domain': u'ndomain',
u'protpos': 1854,
u'rel_prot_pos': 0.98}},
u'gerp': {u'n': 5.32, u'rs': 844.9, u'rs_pval': 8.78912e-51, u's': 5.32},
u'grantham': 21,
u'isderived': u'TRUE',
u'isknownvariant': u'FALSE',
u'istv': u'FALSE',
u'length': 0,
u'mapability': {u'20bp': 1, u'35bp': 1},
u'min_dist_tse': 95,
u'min_dist_tss': 78343,
u'mirsvr': {u'aln': 145, u'e': -17.34, u'score': -0.0965},
u'mutindex': 37,
u'naa': u'M',
u'oaa': u'V',
u'phast_cons': {u'mammalian': 0.998,
u'primate': 0.975,
u'vertebrate': 1.0},
u'phred': 33,
u'phylop': {u'mammalian': 2.766, u'primate': 0.559, u'vertebrate': 3.085},
u'polyphen': {u'cat': u'probably_damaging', u'val': 0.957},
u'pos': 41197790,
u'rawscore': 6.842841,
u'ref': u'C',
u'segway': u'TF2',
u'sift': {u'cat': u'deleterious', u'val': 0},
u'type': u'SNV'},
u'clinvar': {u'allele_id': 70265,
u'alt': u'T',
u'chrom': u'17',
u'cytogenic': u'17q21.31',
u'gene': {u'id': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41197790, u'start': 41197790},
u'hg38': {u'end': 43045773, u'start': 43045773},
u'hgvs': {u'coding': [u'LRG_292t1:c.5497G>A',
u'NM_007299.3:c.*11G>A',
u'NM_007294.3:c.5497G>A'],
u'genomic': [u'LRG_292:g.172211G>A',
u'NG_005905.2:g.172211G>A',
u'NC_000017.11:g.43045773C>T',
u'NC_000017.10:g.41197790C>T']},
u'rcv': [{u'accession': u'RCV000049017',
u'clinical_significance': u'not provided',
u'conditions': {u'identifiers': {u'medgen': u'C0346153',
u'omim': u'114480'},
u'name': u'Familial cancer of breast',
u'synonyms': [u'CHEK2-Related Breast Cancer',
u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer']},
u'last_evaluated': u'2013-02-01',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5497G>A (p.Val1833Met)',
u'review_status': u'no assertion provided'},
{u'accession': u'RCV000077626',
u'clinical_significance': u'Conflicting interpretations of pathogenicity',
u'conditions': {u'age_of_onset': u'All ages',
u'identifiers': {u'medgen': u'C2676676',
u'omim': u'604370',
u'orphanet': u'145'},
u'name': u'Breast-ovarian cancer, familial 1 (BROVCA1)',
u'synonyms': [u'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'OVARIAN CANCER, SUSCEPTIBILITY TO',
u'BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'Breast cancer, familial 1',
u'hereditary breast and ovarian cancer, BROVCA1',
u'Breast-ovarian cancer, familial, 1']},
u'last_evaluated': u'2012-10-15',
u'number_submitters': 2,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5497G>A (p.Val1833Met)',
u'review_status': u'no assertion criteria provided'},
{u'accession': u'RCV000132307',
u'clinical_significance': u'Likely pathogenic',
u'conditions': {u'identifiers': {u'medgen': u'C0027672'},
u'name': u'Hereditary cancer-predisposing syndrome',
u'synonyms': u'Neoplastic Syndromes, Hereditary'},
u'last_evaluated': u'2014-05-02',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5497G>A (p.Val1833Met)',
u'review_status': u'criteria provided, single submitter'}],
u'ref': u'C',
u'rsid': u'rs80357268',
u'type': u'single nucleotide variant',
u'variant_id': 55598},
u'dbnsfp': {u'aa': {u'alt': u'M',
u'codonpos': 1,
u'pos': [u'1833',
u'691',
u'143',
u'324',
u'66',
u'1786',
u'1854',
u'729'],
u'ref': u'V',
u'refcodon': u'GTG'},
u'alt': u'T',
u'ancestral_allele': u'C',
u'cds_strand': u'-',
u'chrom': u'17',
u'clinvar': {u'clinsig': 4,
u'rs': u'rs80357268',
u'trait': u'Hereditary_cancer-predisposing_syndrome'},
u'ensembl': {u'geneid': u'ENSG00000012048',
u'proteinid': [u'ENSP00000350283',
u'ENSP00000312236',
u'ENSP00000465818',
u'ENSP00000467329',
u'ENSP00000465347',
u'ENSP00000418775',
u'ENSP00000418960',
u'ENSP00000420705'],
u'transcriptid': [u'ENST00000357654',
u'ENST00000352993',
u'ENST00000586385',
u'ENST00000591534',
u'ENST00000591849',
u'ENST00000493795',
u'ENST00000471181',
u'ENST00000491747']},
u'fathmm': {u'pred': [u'D', u'D', u'D', u'D', u'D', u'D', u'D', u'D'],
u'rankscore': 0.95286,
u'score': [-3.68, -3.68, -3.68, -3.68, -3.68, -3.68, -3.68, -3.68]},
u'fathmm-mkl': {u'coding_group': u'AEFBI',
u'coding_pred': u'D',
u'coding_rankscore': 0.52871,
u'coding_score': 0.91246},
u'genename': u'BRCA1',
u'gerp++': {u'nr': 5.32, u'rs': 5.32, u'rs_rankscore': 0.75224},
u'gm12878': {u'confidence_value': 0,
u'fitcons_rankscore': 0.89268,
u'fitcons_score': 0.724815},
u'h1-hesc': {u'confidence_value': 0,
u'fitcons_rankscore': 0.96044,
u'fitcons_score': 0.743671},
u'hg18': {u'end': 38451316, u'start': 38451316},
u'hg19': {u'end': 41197790, u'start': 41197790},
u'hg38': {u'end': 43045773, u'start': 43045773},
u'huvec': {u'confidence_value': 0,
u'fitcons_rankscore': 0.52682,
u'fitcons_score': 0.635551},
u'integrated': {u'confidence_value': 0,
u'fitcons_rankscore': 0.92359,
u'fitcons_score': 0.732398},
u'interpro_domain': u'BRCT domain',
u'lrt': {u'converted_rankscore': 0.47273,
u'omega': 0.0,
u'pred': u'D',
u'score': 0.000226},
u'metalr': {u'pred': u'D', u'rankscore': 0.96404, u'score': 0.8916},
u'metasvm': {u'pred': u'D', u'rankscore': 0.96424, u'score': 0.9519},
u'mutationassessor': {u'pred': u'M',
u'rankscore': 0.72894,
u'score': 2.215},
u'mutationtaster': {u'AAE': [u'V1833M',
u'V143M',
u'V324M',
u'V66M',
u'V1786M',
u'V1854M',
u'V729M',
u'V691M',
u'V650M',
u'V682M',
u'V1537M',
u'.',
u'V1568M',
u'V1594M'],
u'converted_rankscore': 0.81033,
u'model': [u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'simple_aae',
u'without_aae',
u'simple_aae',
u'simple_aae'],
u'pred': [u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'D',
u'N',
u'N'],
u'score': [0.999688,
0.999766,
0.999766,
0.999766,
0.999768,
0.99859,
0.999766,
0.999766,
0.999766,
0.999766,
0.99766,
1,
0.897669,
0.897669]},
u'phastcons': {u'20way': {u'mammalian': 0.86,
u'mammalian_rankscore': 0.35735},
u'7way': {u'vertebrate': 0.976, u'vertebrate_rankscore': 0.4664}},
u'phylo': {u'p20way': {u'mammalian': 0.935,
u'mammalian_rankscore': 0.48811},
u'p7way': {u'vertebrate': 0.871, u'vertebrate_rankscore': 0.44667}},
u'polyphen2': {u'hdiv': {u'pred': u'D',
u'rankscore': 0.89865,
u'score': 1.0},
u'hvar': {u'pred': u'D',
u'rankscore': 0.91584,
u'score': [0.999, 0.998, 0.999, 0.999, 0.999, 0.999]}},
u'provean': {u'pred': [u'N', u'N', u'.', u'.', u'.', u'N', u'N', u'N'],
u'rankscore': 0.53216,
u'score': [-0.55, -2.43, None, None, None, -0.54, -0.49, -2.43]},
u'ref': u'C',
u'reliability_index': 10,
u'rsid': u'rs80357268',
u'sift': {u'converted_rankscore': 0.91219,
u'pred': [u'D', u'D', u'.', u'.', u'.', u'D', u'D', u'D'],
u'score': [0.0, 0.001, None, None, None, 0.0, 0.002, 0.001]},
u'siphy_29way': {u'logodds': 14.3724,
u'logodds_rankscore': 0.66207,
u'pi': {u'a': 0.0, u'c': 1.0, u'g': 0.0, u't': 0.0}},
u'uniprot': [{u'acc': u'B4DES0', u'pos': u'682'},
{u'acc': u'C6YB45', u'pos': u'143'},
{u'acc': u'E7ETR2', u'pos': u'728'},
{u'acc': u'E9PFC7', u'pos': u'1855'},
{u'acc': u'P38398', u'pos': u'1833'},
{u'acc': u'P38398-2', u'pos': u'1833'}]},
u'dbsnp': {u'allele_origin': u'unspecified',
u'alleles': [{u'allele': u'C'}, {u'allele': u'T'}],
u'alt': u'T',
u'chrom': u'17',
u'class': u'SNV',
u'dbsnp_build': 132,
u'flags': [u'ASP',
u'LSD',
u'NSM',
u'PM',
u'REF',
u'RV',
u'S3D',
u'SLO',
u'U3'],
u'gene': {u'geneid': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41197791, u'start': 41197790},
u'ref': u'C',
u'rsid': u'rs80357268',
u'validated': False,
u'var_subtype': u'ts',
u'vartype': u'snp'},
u'mutdb': {u'alt': u'A',
u'chrom': u'17',
u'hg19': {u'end': 41197790, u'start': 41197790},
u'mutpred_score': 0.585,
u'ref': u'G',
u'rsid': u'rs80357268',
u'strand': u'm'},
u'snpeff': {u'ann': [{u'cdna': {u'length': u'7270', u'position': u'5792'},
u'cds': {u'length': u'5655', u'position': u'5560'},
u'effect': u'missense_variant',
u'feature_id': u'NM_007300.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5560G>A',
u'hgvs_p': u'p.Val1854Met',
u'protein': {u'length': u'1884', u'position': u'1854'},
u'putative_impact': u'MODERATE',
u'rank': u'24',
u'total': u'24',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'3682', u'position': u'2204'},
u'cds': {u'length': u'2280', u'position': u'2185'},
u'effect': u'missense_variant',
u'feature_id': u'NM_007298.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.2185G>A',
u'hgvs_p': u'p.Val729Met',
u'protein': {u'length': u'759', u'position': u'729'},
u'putative_impact': u'MODERATE',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'7115', u'position': u'5637'},
u'cds': {u'length': u'5451', u'position': u'5356'},
u'effect': u'missense_variant',
u'feature_id': u'NM_007297.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5356G>A',
u'hgvs_p': u'p.Val1786Met',
u'protein': {u'length': u'1816', u'position': u'1786'},
u'putative_impact': u'MODERATE',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'7207', u'position': u'5729'},
u'cds': {u'length': u'5592', u'position': u'5497'},
u'effect': u'missense_variant',
u'feature_id': u'NM_007294.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5497G>A',
u'hgvs_p': u'p.Val1833Met',
u'protein': {u'length': u'1863', u'position': u'1833'},
u'putative_impact': u'MODERATE',
u'rank': u'23',
u'total': u'23',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'11',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007299.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*11G>A',
u'putative_impact': u'MODIFIER',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'effect': u'non_coding_exon_variant',
u'feature_id': u'NR_027676.1',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'n.5633G>A',
u'putative_impact': u'MODIFIER',
u'rank': u'23',
u'total': u'23',
u'transcript_biotype': u'Noncoding'}]},
u'vcf': {u'alt': u'T', u'position': u'41197790', u'ref': u'C'}}],
u'max_score': 12.69064,
u'took': 4,
u'total': 3532}
mv.query('clinvar.gene.symbol:BRCA1',fetch_all=True)
<generator object _fetch_all at 0x10b99fb90>
out = mv.query('clinvar.gene.symbol:BRCA1 AND clinvar.rcv.clinical_significance:pathogenic')
Now, only 1126 variants are left matching these two criteria.out
{u'hits': [{u'_id': u'chr17:g.41197590_41197593del',
u'_score': 15.629933,
u'clinvar': {u'allele_id': 102794,
u'alt': u'-',
u'chrom': u'17',
u'cytogenic': u'17q21.31',
u'gene': {u'id': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41197593, u'start': 41197590},
u'hg38': {u'end': 43045576, u'start': 43045573},
u'hgvs': {u'coding': [u'LRG_292t1:c.*102_*105delCTGT',
u'NM_007294.3:c.*102_*105delCTGT'],
u'genomic': [u'LRG_292:g.172408_172411delCTGT',
u'NG_005905.2:g.172408_172411delCTGT',
u'NC_000017.11:g.43045573_43045576delACAG',
u'NC_000017.10:g.41197590_41197593delACAG']},
u'rcv': {u'accession': u'RCV000083012',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'age_of_onset': u'All ages',
u'identifiers': {u'medgen': u'C2676676',
u'omim': u'604370',
u'orphanet': u'145'},
u'name': u'Breast-ovarian cancer, familial 1 (BROVCA1)',
u'synonyms': [u'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'OVARIAN CANCER, SUSCEPTIBILITY TO',
u'BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'Breast cancer, familial 1',
u'hereditary breast and ovarian cancer, BROVCA1',
u'Breast-ovarian cancer, familial, 1']},
u'last_evaluated': u'2011-10-17',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.*102_*105delCTGT',
u'review_status': u'no assertion criteria provided'},
u'ref': u'ACAG',
u'rsid': u'rs431825382',
u'type': u'Deletion',
u'variant_id': 96891},
u'snpeff': {u'ann': [{u'distance_to_feature': u'102',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007300.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*102_*105delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'24',
u'total': u'24',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'102',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007298.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*102_*105delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'102',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007297.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*102_*105delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'208',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007299.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*208_*211delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'22',
u'total': u'22',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'102',
u'effect': u'3_prime_UTR_variant',
u'feature_id': u'NM_007294.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.*102_*105delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'23',
u'total': u'23',
u'transcript_biotype': u'Coding'},
{u'effect': u'non_coding_exon_variant',
u'feature_id': u'NR_027676.1',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'n.5830_5833delCTGT',
u'putative_impact': u'MODIFIER',
u'rank': u'23',
u'total': u'23',
u'transcript_biotype': u'Noncoding'}]},
u'vcf': {u'alt': u'G', u'position': u'41197589', u'ref': u'GACAG'}},
{u'_id': u'chr17:g.41203078A>C',
u'_score': 15.629933,
u'clinvar': {u'allele_id': 180821,
u'alt': u'C',
u'chrom': u'17',
u'cytogenic': u'17q21.31',
u'gene': {u'id': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41203078, u'start': 41203078},
u'hg38': {u'end': 43051061, u'start': 43051061},
u'hgvs': {u'coding': [u'LRG_292t1:c.5332+2T>G',
u'NM_007294.3:c.5332+2T>G'],
u'genomic': [u'LRG_292:g.166923T>G',
u'NG_005905.2:g.166923T>G',
u'NC_000017.11:g.43051061A>C',
u'NC_000017.10:g.41203078A>C']},
u'rcv': {u'accession': u'RCV000160004',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'identifiers': {u'medgen': u'C0346153',
u'omim': u'114480'},
u'name': u'Familial cancer of breast',
u'synonyms': [u'CHEK2-Related Breast Cancer',
u'BRCA1 and BRCA2 Hereditary Breast and Ovarian Cancer']},
u'last_evaluated': u'2014-08-20',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.5332+2T>G',
u'review_status': u'criteria provided, single submitter'},
u'ref': u'A',
u'rsid': u'rs80358182',
u'type': u'single nucleotide variant',
u'variant_id': 182168},
u'dbnsfp': {u'aa': {u'pos': -1},
u'alt': u'C',
u'ancestral_allele': u'A',
u'cds_strand': u'-',
u'chrom': u'17',
u'clinvar': {u'clinsig': 5,
u'rs': u'rs80358182',
u'trait': u'Familial_cancer_of_breast'},
u'ensembl': {u'geneid': u'ENSG00000012048',
u'proteinid': [u'ENSP00000350283',
u'ENSP00000312236',
u'ENSP00000417148',
u'ENSP00000465818',
u'ENSP00000467329',
u'ENSP00000418775',
u'ENSP00000418960',
u'ENSP00000420705'],
u'transcriptid': [u'ENST00000357654',
u'ENST00000352993',
u'ENST00000468300',
u'ENST00000586385',
u'ENST00000591534',
u'ENST00000493795',
u'ENST00000471181',
u'ENST00000491747']},
u'fathmm-mkl': {u'coding_group': u'AEFBI',
u'coding_pred': u'D',
u'coding_rankscore': 0.72135,
u'coding_score': 0.97037},
u'genename': u'BRCA1',
u'gerp++': {u'nr': 5.21, u'rs': 5.21, u'rs_rankscore': 0.71834},
u'gm12878': {u'confidence_value': 0,
u'fitcons_rankscore': 0.04603,
u'fitcons_score': 0.30413},
u'h1-hesc': {u'confidence_value': 0,
u'fitcons_rankscore': 0.03107,
u'fitcons_score': 0.137589},
u'hg18': {u'end': 38456604, u'start': 38456604},
u'hg19': {u'end': 41203078, u'start': 41203078},
u'hg38': {u'end': 43051061, u'start': 43051061},
u'huvec': {u'confidence_value': 0,
u'fitcons_rankscore': 0.02674,
u'fitcons_score': 0.109871},
u'integrated': {u'confidence_value': 0,
u'fitcons_rankscore': 0.0442,
u'fitcons_score': 0.295142},
u'mutationtaster': {u'converted_rankscore': 0.81033,
u'model': u'without_aae',
u'pred': u'D',
u'score': 1},
u'phastcons': {u'20way': {u'mammalian': 0.989,
u'mammalian_rankscore': 0.53465},
u'7way': {u'vertebrate': 0.996, u'vertebrate_rankscore': 0.63571}},
u'phylo': {u'p20way': {u'mammalian': 1.199,
u'mammalian_rankscore': 0.95998},
u'p7way': {u'vertebrate': 1.062, u'vertebrate_rankscore': 0.92612}},
u'ref': u'A',
u'siphy_29way': {u'logodds': 11.6541,
u'logodds_rankscore': 0.50308,
u'pi': {u'a': 1.0, u'c': 0.0, u'g': 0.0, u't': 0.0}}},
u'dbsnp': {u'allele_origin': u'unspecified',
u'alleles': [{u'allele': u'A'}, {u'allele': u'C'}, {u'allele': u'T'}],
u'alt': u'C',
u'chrom': u'17',
u'class': u'SNV',
u'dbsnp_build': 132,
u'flags': [u'ASP', u'DSS', u'LSD', u'PM', u'RV', u'SLO'],
u'gene': {u'geneid': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41203079, u'start': 41203078},
u'ref': u'A',
u'rsid': u'rs80358182',
u'validated': False,
u'var_subtype': u'unknown',
u'vartype': u'snp'},
u'snpeff': {u'ann': [{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NM_007300.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5395+2T>G',
u'putative_impact': u'HIGH',
u'rank': u'21',
u'total': u'23',
u'transcript_biotype': u'Coding'},
{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NM_007298.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.2020+2T>G',
u'putative_impact': u'HIGH',
u'rank': u'19',
u'total': u'21',
u'transcript_biotype': u'Coding'},
{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NR_027676.1',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'n.5468+2T>G',
u'putative_impact': u'HIGH',
u'rank': u'20',
u'total': u'22',
u'transcript_biotype': u'Noncoding'},
{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NM_007297.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5191+2T>G',
u'putative_impact': u'HIGH',
u'rank': u'19',
u'total': u'21',
u'transcript_biotype': u'Coding'},
{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NM_007299.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.2020+2T>G',
u'putative_impact': u'HIGH',
u'rank': u'20',
u'total': u'21',
u'transcript_biotype': u'Coding'},
{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NM_007294.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.5332+2T>G',
u'putative_impact': u'HIGH',
u'rank': u'20',
u'total': u'22',
u'transcript_biotype': u'Coding'}],
u'lof': {u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'number_of_transcripts_in_gene': u'6',
u'percent_of_transcripts_affected': u'0.83'}},
u'vcf': {u'alt': u'C', u'position': u'41203078', u'ref': u'A'}},
{u'_id': u'chr17:g.41226347C>A',
u'_score': 15.629933,
u'clinvar': {u'allele_id': 184911,
u'alt': u'A',
u'chrom': u'17',
u'cytogenic': u'17q21.31',
u'gene': {u'id': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41226347, u'start': 41226347},
u'hg38': {u'end': 43074330, u'start': 43074330},
u'hgvs': {u'coding': [u'LRG_292t1:c.4675+1G>T',
u'NM_007294.3:c.4675+1G>T'],
u'genomic': [u'LRG_292:g.143654G>T',
u'NG_005905.2:g.143654G>T',
u'NC_000017.11:g.43074330C>A',
u'NC_000017.10:g.41226347C>A']},
u'rcv': {u'accession': u'RCV000164823',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'identifiers': {u'medgen': u'C0027672'},
u'name': u'Hereditary cancer-predisposing syndrome',
u'synonyms': u'Neoplastic Syndromes, Hereditary'},
u'last_evaluated': u'2014-06-12',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.4675+1G>T',
u'review_status': u'criteria provided, single submitter'},
u'ref': u'C',
u'rsid': u'rs80358044',
u'type': u'single nucleotide variant',
u'variant_id': 185411},
u'dbnsfp': {u'aa': {u'pos': -1},
u'alt': u'A',
u'ancestral_allele': u'C',
u'cds_strand': u'-',
u'chrom': u'17',
u'ensembl': {u'geneid': u'ENSG00000012048',
u'proteinid': [u'ENSP00000350283',
u'ENSP00000312236',
u'ENSP00000417148',
u'ENSP00000467329',
u'ENSP00000418775',
u'ENSP00000418960',
u'ENSP00000420705',
u'ENSP00000419481',
u'ENSP00000420412',
u'ENSP00000418819'],
u'transcriptid': [u'ENST00000357654',
u'ENST00000352993',
u'ENST00000468300',
u'ENST00000591534',
u'ENST00000493795',
u'ENST00000471181',
u'ENST00000491747',
u'ENST00000484087',
u'ENST00000478531',
u'ENST00000493919']},
u'fathmm-mkl': {u'coding_group': u'AEFBI',
u'coding_pred': u'D',
u'coding_rankscore': 0.49073,
u'coding_score': 0.89096},
u'genename': u'BRCA1',
u'gerp++': {u'nr': 5.54, u'rs': 4.57, u'rs_rankscore': 0.55615},
u'gm12878': {u'confidence_value': 0,
u'fitcons_rankscore': 0.04603,
u'fitcons_score': 0.30413},
u'h1-hesc': {u'confidence_value': 0,
u'fitcons_rankscore': 0.03107,
u'fitcons_score': 0.137589},
u'hg18': {u'end': 38479873, u'start': 38479873},
u'hg19': {u'end': 41226347, u'start': 41226347},
u'hg38': {u'end': 43074330, u'start': 43074330},
u'huvec': {u'confidence_value': 0,
u'fitcons_rankscore': 0.02369,
u'fitcons_score': 0.09929},
u'integrated': {u'confidence_value': 0,
u'fitcons_rankscore': 0.0442,
u'fitcons_score': 0.295142},
u'mutationtaster': {u'converted_rankscore': 0.81033,
u'model': u'without_aae',
u'pred': u'D',
u'score': 1},
u'phastcons': {u'20way': {u'mammalian': 0.995,
u'mammalian_rankscore': 0.60234},
u'7way': {u'vertebrate': 0.437, u'vertebrate_rankscore': 0.24756}},
u'phylo': {u'p20way': {u'mammalian': 0.928,
u'mammalian_rankscore': 0.43604},
u'p7way': {u'vertebrate': 0.871, u'vertebrate_rankscore': 0.44667}},
u'ref': u'C',
u'siphy_29way': {u'logodds': 10.2876,
u'logodds_rankscore': 0.4249,
u'pi': {u'a': 0.0, u'c': 0.9116, u'g': 0.0, u't': 0.0884}}},
u'dbsnp': {u'allele_origin': u'unspecified',
u'alleles': [{u'allele': u'C'}, {u'allele': u'A'}, {u'allele': u'T'}],
u'alt': u'A',
u'chrom': u'17',
u'class': u'SNV',
u'dbsnp_build': 132,
u'flags': [u'ASP', u'DSS', u'LSD', u'PM', u'RV', u'SLO'],
u'gene': {u'geneid': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41226348, u'start': 41226347},
u'ref': u'C',
u'rsid': u'rs80358044',
u'validated': False,
u'var_subtype': u'unknown',
u'vartype': u'snp'},
u'snpeff': {u'ann': [{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NM_007300.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.4738+1G>T',
u'putative_impact': u'HIGH',
u'rank': u'15',
u'total': u'23',
u'transcript_biotype': u'Coding'},
{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NM_007298.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.1363+1G>T',
u'putative_impact': u'HIGH',
u'rank': u'13',
u'total': u'21',
u'transcript_biotype': u'Coding'},
{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NR_027676.1',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'n.4811+1G>T',
u'putative_impact': u'HIGH',
u'rank': u'14',
u'total': u'22',
u'transcript_biotype': u'Noncoding'},
{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NM_007297.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.4534+1G>T',
u'putative_impact': u'HIGH',
u'rank': u'13',
u'total': u'21',
u'transcript_biotype': u'Coding'},
{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NM_007299.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.1363+1G>T',
u'putative_impact': u'HIGH',
u'rank': u'14',
u'total': u'21',
u'transcript_biotype': u'Coding'},
{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NM_007294.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.4675+1G>T',
u'putative_impact': u'HIGH',
u'rank': u'14',
u'total': u'22',
u'transcript_biotype': u'Coding'}],
u'lof': {u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'number_of_transcripts_in_gene': u'6',
u'percent_of_transcripts_affected': u'0.83'}},
u'vcf': {u'alt': u'A', u'position': u'41226347', u'ref': u'C'}},
{u'_id': u'chr17:g.41228600G>C',
u'_score': 15.629933,
u'cadd': {u'_license': u'http://goo.gl/bkpNhq',
u'alt': u'C',
u'anc': u'G',
u'annotype': u'CodingTranscript',
u'bstatistic': 115,
u'chmm': {u'bivflnk': 0.0,
u'enh': 0.0,
u'enhbiv': 0.0,
u'het': 0.0,
u'quies': 0.276,
u'reprpc': 0.0,
u'reprpcwk': 0.0,
u'tssa': 0.0,
u'tssaflnk': 0.0,
u'tssbiv': 0.0,
u'tx': 0.094,
u'txflnk': 0.0,
u'txwk': 0.63,
u'znfrpts': 0.0},
u'chrom': 17,
u'consdetail': u'stop_gained',
u'consequence': u'STOP_GAINED',
u'consscore': 8,
u'cpg': 0.0,
u'dna': {u'helt': -1.31, u'mgw': 0.61, u'prot': -2.21, u'roll': 5.92},
u'encode': {u'exp': 169.31,
u'h3k27ac': 5.0,
u'h3k4me1': 2.24,
u'h3k4me3': 4.68,
u'nucleo': 1.5},
u'exon': u'14/24',
u'fitcons': 0.723164,
u'gc': 0.36,
u'gene': {u'ccds_id': u'CCDS11456.2',
u'cds': {u'cdna_pos': 4684,
u'cds_pos': 4452,
u'rel_cdna_pos': 0.79,
u'rel_cds_pos': 0.79},
u'feature_id': u'ENST00000471181',
u'gene_id': u'ENSG00000012048',
u'genename': u'BRCA1',
u'prot': {u'domain': u'ndomain',
u'protpos': 1484,
u'rel_prot_pos': 0.79}},
u'gerp': {u'n': 4.97, u'rs': 545.1, u'rs_pval': 1.49133e-29, u's': 2.76},
u'isderived': u'TRUE',
u'isknownvariant': u'FALSE',
u'istv': u'TRUE',
u'length': 0,
u'mapability': {u'20bp': 1, u'35bp': 1},
u'min_dist_tse': 46,
u'min_dist_tss': 15242,
u'mutindex': 60,
u'naa': u'*',
u'oaa': u'Y',
u'phast_cons': {u'mammalian': 0.012,
u'primate': 0.625,
u'vertebrate': 0.009},
u'phred': 36,
u'phylop': {u'mammalian': 0.391, u'primate': -0.348, u'vertebrate': 0.626},
u'pos': 41228600,
u'rawscore': 9.620885,
u'ref': u'G',
u'segway': u'TF1',
u'type': u'SNV'},
u'clinvar': {u'allele_id': 152550,
u'alt': u'C',
u'chrom': u'17',
u'cytogenic': u'17q21.31',
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u'hg19': {u'end': 41228600, u'start': 41228600},
u'hg38': {u'end': 43076583, u'start': 43076583},
u'hgvs': {u'coding': [u'LRG_292t1:c.4389C>G', u'NM_007294.3:c.4389C>G'],
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u'NG_005905.2:g.141401C>G',
u'NC_000017.11:g.43076583G>C',
u'NC_000017.10:g.41228600G>C']},
u'rcv': {u'accession': u'RCV000132271',
u'clinical_significance': u'Pathogenic',
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u'synonyms': u'Neoplastic Syndromes, Hereditary'},
u'last_evaluated': u'2014-03-24',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.4389C>G (p.Tyr1463Ter)',
u'review_status': u'criteria provided, single submitter'},
u'ref': u'G',
u'rsid': u'rs80356997',
u'type': u'single nucleotide variant',
u'variant_id': 142836},
u'dbnsfp': {u'aa': {u'alt': u'X',
u'codonpos': 3,
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u'refcodon': u'TAC'},
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u'chrom': u'17',
u'clinvar': {u'clinsig': 5,
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u'trait': u'Hereditary_cancer-predisposing_syndrome'},
u'ensembl': {u'geneid': u'ENSG00000012048',
u'proteinid': [u'ENSP00000350283',
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u'ENSP00000417148',
u'ENSP00000418775',
u'ENSP00000418960',
u'ENSP00000420705',
u'ENSP00000419481',
u'ENSP00000420412',
u'ENSP00000418819',
u'ENSP00000418212'],
u'transcriptid': [u'ENST00000357654',
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u'ENST00000493795',
u'ENST00000471181',
u'ENST00000491747',
u'ENST00000484087',
u'ENST00000478531',
u'ENST00000493919',
u'ENST00000487825']},
u'fathmm-mkl': {u'coding_group': u'AEFBI',
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u'fitcons_score': 0.709663},
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u'huvec': {u'confidence_value': 0,
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u'fitcons_score': 0.732398},
u'interpro_domain': u'BRCA1, serine-rich domain',
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u'omega': 0.956183,
u'pred': u'N',
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u'mutationtaster': {u'AAE': [u'Y1463*',
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u'Y1416*',
u'Y1484*',
u'Y359*',
u'Y321*',
u'Y280*',
u'Y312*',
u'Y1167*',
u'.',
u'.',
u'.',
u'.',
u'.'],
u'converted_rankscore': 0.81033,
u'model': [u'complex_aae',
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u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
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u'A',
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u'A',
u'A',
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1,
1,
1,
1,
1,
1,
1,
0.999999,
0.999999,
0.999999,
0.999999,
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u'phastcons': {u'20way': {u'mammalian': 0.132,
u'mammalian_rankscore': 0.19814},
u'7way': {u'vertebrate': 0.086, u'vertebrate_rankscore': 0.16273}},
u'phylo': {u'p20way': {u'mammalian': -0.134,
u'mammalian_rankscore': 0.10964},
u'p7way': {u'vertebrate': 0.091, u'vertebrate_rankscore': 0.25623}},
u'ref': u'G',
u'rsid': u'rs80356997',
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u'logodds_rankscore': 0.19833,
u'pi': {u'a': 0.8017, u'c': 0.0, u'g': 0.1983, u't': 0.0}}},
u'dbsnp': {u'allele_origin': u'unspecified',
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{u'allele': u'T'}],
u'alt': u'C',
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u'dbsnp_build': 132,
u'flags': [u'ASP', u'LSD', u'NOV', u'PM', u'REF', u'RV', u'SLO', u'SYN'],
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u'hg19': {u'end': 41228601, u'start': 41228600},
u'ref': u'G',
u'rsid': u'rs80356997',
u'validated': False,
u'var_subtype': u'unknown',
u'vartype': u'snp'},
u'snpeff': {u'ann': [{u'cdna': {u'length': u'7270', u'position': u'4684'},
u'cds': {u'length': u'5655', u'position': u'4452'},
u'effect': u'stop_gained',
u'feature_id': u'NM_007300.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.4452C>G',
u'hgvs_p': u'p.Tyr1484*',
u'protein': {u'length': u'1884', u'position': u'1484'},
u'putative_impact': u'HIGH',
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u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.1077C>G',
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u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.4248C>G',
u'hgvs_p': u'p.Tyr1416*',
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{u'cdna': {u'length': u'3783', u'position': u'1271'},
u'cds': {u'length': u'2100', u'position': u'1077'},
u'effect': u'stop_gained',
u'feature_id': u'NM_007299.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.1077C>G',
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{u'cdna': {u'length': u'7207', u'position': u'4621'},
u'cds': {u'length': u'5592', u'position': u'4389'},
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u'lof': {u'gene_id': u'BRCA1',
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u'number_of_transcripts_in_gene': u'6',
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u'nmd': {u'gene_id': u'BRCA1',
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u'vcf': {u'alt': u'C', u'position': u'41228600', u'ref': u'G'}},
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u'clinvar': {u'allele_id': 131221,
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u'hg38': {u'end': 43090962, u'start': 43090961},
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u'rcv': {u'accession': u'RCV000112274',
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u'last_evaluated': u'2002-05-29',
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u'alt': u'CCT',
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u'hg19': {u'end': 41242979, u'start': 41242978},
u'ref': u'C',
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u'validated': False,
u'var_subtype': u'ins',
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u'snpeff': {u'ann': [{u'cdna': {u'length': u'7270', u'position': u'4399'},
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u'hgvs_c': u'c.4026_4027insAG',
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u'lof': {u'gene_id': u'BRCA1',
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u'number_of_transcripts_in_gene': u'6',
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u'vcf': {u'alt': u'CCT', u'position': u'41242978', u'ref': u'C'}},
{u'_id': u'chr17:g.41243718_41243718dupG',
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u'clinvar': {u'allele_id': 131193,
u'alt': u'GG',
u'chrom': u'17',
u'cytogenic': u'17q21.31',
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u'hg19': {u'end': 41243718, u'start': 41243718},
u'hg38': {u'end': 43091701, u'start': 43091701},
u'hgvs': {u'coding': [u'NM_007294.3:c.3830_3831insC',
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u'NM_007294.3:c.3830dupC'],
u'genomic': [u'NG_005905.2:g.126283_126284insC',
u'LRG_292:g.126283dupC',
u'NG_005905.2:g.126283dupC',
u'NC_000017.11:g.43091701dupG',
u'NC_000017.10:g.41243718dupG']},
u'rcv': {u'accession': u'RCV000112193',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'age_of_onset': u'All ages',
u'identifiers': {u'medgen': u'C2676676',
u'omim': u'604370',
u'orphanet': u'145'},
u'name': u'Breast-ovarian cancer, familial 1 (BROVCA1)',
u'synonyms': [u'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'OVARIAN CANCER, SUSCEPTIBILITY TO',
u'BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'Breast cancer, familial 1',
u'hereditary breast and ovarian cancer, BROVCA1',
u'Breast-ovarian cancer, familial, 1']},
u'last_evaluated': u'2002-06-20',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.3830dupC (p.Ala1279Glyfs)',
u'review_status': u'no assertion criteria provided'},
u'ref': u'G',
u'rsid': u'rs80357878',
u'type': u'Duplication',
u'variant_id': 125655}},
{u'_id': u'chr17:g.41244224_41244225del',
u'_score': 15.629933,
u'clinvar': {u'allele_id': 184975,
u'alt': u'-',
u'chrom': u'17',
u'cytogenic': u'17q21.31',
u'gene': {u'id': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41244225, u'start': 41244224},
u'hg38': {u'end': 43092208, u'start': 43092207},
u'hgvs': {u'coding': [u'LRG_292t1:c.3323_3324delTA',
u'NM_007294.3:c.3323_3324delTA',
u'NM_007298.3:c.788-1176_788-1175del'],
u'genomic': [u'LRG_292:g.125776_125777delTA',
u'NG_005905.2:g.125776_125777delTA',
u'NC_000017.11:g.43092207_43092208delTA',
u'NC_000017.10:g.41244224_41244225delTA']},
u'rcv': {u'accession': u'RCV000165779',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'identifiers': {u'medgen': u'C0027672'},
u'name': u'Hereditary cancer-predisposing syndrome',
u'synonyms': u'Neoplastic Syndromes, Hereditary'},
u'last_evaluated': u'2014-08-26',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.3323_3324delTA (p.Ile1108Lysfs)',
u'review_status': u'criteria provided, single submitter'},
u'ref': u'TA',
u'rsid': u'rs786202791',
u'type': u'Deletion',
u'variant_id': 186225},
u'snpeff': {u'ann': [{u'cdna': {u'length': u'7270', u'position': u'3556'},
u'cds': {u'length': u'5655', u'position': u'3323'},
u'effect': u'frameshift_variant',
u'feature_id': u'NM_007300.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.3323_3324delTA',
u'hgvs_p': u'p.Ile1108fs',
u'protein': {u'length': u'1884', u'position': u'1108'},
u'putative_impact': u'HIGH',
u'rank': u'10',
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u'transcript_biotype': u'Coding'},
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u'feature_id': u'NM_007297.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
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u'NG_005905.2:g.118210G>A',
u'NC_000017.11:g.43099774C>T',
u'NC_000017.10:g.41251791C>T']},
u'rcv': {u'accession': u'RCV000112729',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'age_of_onset': u'All ages',
u'identifiers': {u'medgen': u'C2676676',
u'omim': u'604370',
u'orphanet': u'145'},
u'name': u'Breast-ovarian cancer, familial 1 (BROVCA1)',
u'synonyms': [u'BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'OVARIAN CANCER, SUSCEPTIBILITY TO',
u'BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 1',
u'Breast cancer, familial 1',
u'hereditary breast and ovarian cancer, BROVCA1',
u'Breast-ovarian cancer, familial, 1']},
u'last_evaluated': u'2003-12-23',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_007294.3(BRCA1):c.547+1G>A',
u'review_status': u'no assertion criteria provided'},
u'ref': u'C',
u'rsid': u'rs80358030',
u'type': u'single nucleotide variant',
u'variant_id': 125881},
u'dbnsfp': {u'aa': {u'pos': -1},
u'alt': u'T',
u'ancestral_allele': u'C',
u'cds_strand': u'-',
u'chrom': u'17',
u'clinvar': {u'clinsig': 5,
u'rs': u'rs80358030',
u'trait': u'Breast-ovarian_cancer\\x2c_familial_1'},
u'ensembl': {u'geneid': u'ENSG00000012048',
u'proteinid': [u'ENSP00000350283',
u'ENSP00000312236',
u'ENSP00000417148',
u'ENSP00000418775',
u'ENSP00000418960',
u'ENSP00000420705',
u'ENSP00000419481',
u'ENSP00000420412',
u'ENSP00000418819',
u'ENSP00000418212',
u'ENSP00000326002',
u'ENSP00000419274',
u'ENSP00000419988',
u'ENSP00000419103',
u'ENSP00000417554'],
u'transcriptid': [u'ENST00000357654',
u'ENST00000352993',
u'ENST00000468300',
u'ENST00000493795',
u'ENST00000471181',
u'ENST00000491747',
u'ENST00000484087',
u'ENST00000478531',
u'ENST00000493919',
u'ENST00000487825',
u'ENST00000354071',
u'ENST00000470026',
u'ENST00000477152',
u'ENST00000494123',
u'ENST00000476777']},
u'fathmm-mkl': {u'coding_group': u'AEFBI',
u'coding_pred': u'D',
u'coding_rankscore': 0.45601,
u'coding_score': 0.86583},
u'genename': u'BRCA1',
u'gerp++': {u'nr': 5.16, u'rs': 5.16, u'rs_rankscore': 0.70385},
u'gm12878': {u'confidence_value': 0,
u'fitcons_rankscore': 0.02865,
u'fitcons_score': 0.156173},
u'h1-hesc': {u'confidence_value': 0,
u'fitcons_rankscore': 0.02788,
u'fitcons_score': 0.125526},
u'hg18': {u'end': 38505317, u'start': 38505317},
u'hg19': {u'end': 41251791, u'start': 41251791},
u'hg38': {u'end': 43099774, u'start': 43099774},
u'huvec': {u'confidence_value': 0,
u'fitcons_rankscore': 0.02238,
u'fitcons_score': 0.092715},
u'integrated': {u'confidence_value': 0,
u'fitcons_rankscore': 0.02649,
u'fitcons_score': 0.156188},
u'mutationtaster': {u'converted_rankscore': 0.81033,
u'model': u'without_aae',
u'pred': u'D',
u'score': 1},
u'phastcons': {u'20way': {u'mammalian': 0.898,
u'mammalian_rankscore': 0.37771},
u'7way': {u'vertebrate': 0.559, u'vertebrate_rankscore': 0.26867}},
u'phylo': {u'p20way': {u'mammalian': 0.892,
u'mammalian_rankscore': 0.4006},
u'p7way': {u'vertebrate': 0.871, u'vertebrate_rankscore': 0.44667}},
u'ref': u'C',
u'rsid': u'rs80358030',
u'siphy_29way': {u'logodds': 14.3275,
u'logodds_rankscore': 0.6588,
u'pi': {u'a': 0.0, u'c': 1.0, u'g': 0.0, u't': 0.0}}},
u'dbsnp': {u'allele_origin': u'unspecified',
u'alleles': [{u'allele': u'C'}, {u'allele': u'A'}, {u'allele': u'T'}],
u'alt': u'T',
u'chrom': u'17',
u'class': u'SNV',
u'dbsnp_build': 132,
u'flags': [u'ASP', u'DSS', u'LSD', u'PM', u'RV', u'SLO'],
u'gene': {u'geneid': u'672', u'symbol': u'BRCA1'},
u'hg19': {u'end': 41251792, u'start': 41251791},
u'ref': u'C',
u'rsid': u'rs80358030',
u'validated': False,
u'var_subtype': u'unknown',
u'vartype': u'snp'},
u'snpeff': {u'ann': [{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NM_007300.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.547+1G>A',
u'putative_impact': u'HIGH',
u'rank': u'7',
u'total': u'23',
u'transcript_biotype': u'Coding'},
{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NM_007298.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.547+1G>A',
u'putative_impact': u'HIGH',
u'rank': u'6',
u'total': u'21',
u'transcript_biotype': u'Coding'},
{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NR_027676.1',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'n.683+1G>A',
u'putative_impact': u'HIGH',
u'rank': u'7',
u'total': u'22',
u'transcript_biotype': u'Noncoding'},
{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NM_007297.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.406+1G>A',
u'putative_impact': u'HIGH',
u'rank': u'6',
u'total': u'21',
u'transcript_biotype': u'Coding'},
{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NM_007299.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.547+1G>A',
u'putative_impact': u'HIGH',
u'rank': u'7',
u'total': u'21',
u'transcript_biotype': u'Coding'},
{u'effect': u'splice_donor_variant&intron_variant',
u'feature_id': u'NM_007294.3',
u'feature_type': u'transcript',
u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'hgvs_c': u'c.547+1G>A',
u'putative_impact': u'HIGH',
u'rank': u'7',
u'total': u'22',
u'transcript_biotype': u'Coding'}],
u'lof': {u'gene_id': u'BRCA1',
u'gene_name': u'BRCA1',
u'number_of_transcripts_in_gene': u'6',
u'percent_of_transcripts_affected': u'0.83'}},
u'vcf': {u'alt': u'T', u'position': u'41251791', u'ref': u'C'}}],
u'max_score': 15.629933,
u'took': 72,
u'total': 1126}
Here is a list of *RCV accession numbers* you might want to query.xli = ['RCV000059118',
'RCV000059119',
'RCV000057234',
'RCV000037456',
'RCV000000019',
'RCV000000134']
out = mv.querymany(xli, scopes='clinvar.rcv.accession')
querying 1-6...done. Finished.
Here is the output of all annotation records related to these *RCV accession numbers* in xli in MyVariant.info.out
[{u'_id': u'chr11:g.118895925C>T',
u'_score': 10.333494,
u'cadd': {u'_license': u'http://goo.gl/bkpNhq',
u'alt': u'T',
u'anc': u'C',
u'annotype': [u'CodingTranscript', u'Intergenic'],
u'bstatistic': 476,
u'chmm': {u'bivflnk': 0.0,
u'enh': 0.197,
u'enhbiv': 0.0,
u'het': 0.0,
u'quies': 0.0,
u'reprpc': 0.0,
u'reprpcwk': 0.0,
u'tssa': 0.0,
u'tssaflnk': 0.0,
u'tssbiv': 0.0,
u'tx': 0.622,
u'txflnk': 0.055,
u'txwk': 0.11,
u'znfrpts': 0.0},
u'chrom': 11,
u'consdetail': [u'missense', u'downstream'],
u'consequence': [u'NON_SYNONYMOUS', u'DOWNSTREAM'],
u'consscore': [7, 1],
u'cpg': 0.04,
u'dna': {u'helt': 2.03, u'mgw': 0.26, u'prot': -2.64, u'roll': -0.64},
u'encode': {u'exp': 136.25,
u'h3k27ac': 13.84,
u'h3k4me1': 33.84,
u'h3k4me3': 6.4,
u'nucleo': 2.7,
u'occ': 2,
u'p_val': {u'comb': 0.95,
u'ctcf': 0.0,
u'dnas': 1.62,
u'faire': 0.0,
u'mycp': 0.0,
u'polii': 0.0},
u'sig': {u'ctcf': 0.03,
u'dnase': 0.04,
u'faire': 0.01,
u'myc': 0.0,
u'polii': 0.0}},
u'exon': u'11/12',
u'fitcons': 0.2838,
u'gc': 0.55,
u'gene': [{u'cds': {u'cdna_pos': 1606,
u'cds_pos': 1165,
u'rel_cdna_pos': 0.68,
u'rel_cds_pos': 0.86},
u'feature_id': u'ENST00000357590',
u'gene_id': u'ENSG00000137700',
u'genename': u'SLC37A4',
u'prot': {u'domain': u'tmhmm', u'protpos': 389, u'rel_prot_pos': 0.86}},
{u'ccds_id': u'CCDS8407.1',
u'feature_id': u'ENST00000533632',
u'gene_id': u'ENSG00000196655',
u'genename': u'TRAPPC4'}],
u'gerp': {u'n': 5.12, u'rs': 2485.2, u'rs_pval': 2.73146e-114, u's': 5.12},
u'grantham': 58,
u'isderived': u'TRUE',
u'isknownvariant': u'FALSE',
u'istv': u'FALSE',
u'length': 0,
u'mapability': {u'20bp': 1, u'35bp': 1},
u'min_dist_tse': 63,
u'min_dist_tss': 3820,
u'mutindex': 109,
u'naa': u'T',
u'oaa': u'A',
u'phast_cons': {u'mammalian': 0.999, u'primate': 0.987, u'vertebrate': 1.0},
u'phred': 34,
u'phylop': {u'mammalian': 2.677, u'primate': 0.557, u'vertebrate': 5.851},
u'polyphen': {u'cat': u'possibly_damaging', u'val': 0.861},
u'pos': 118895925,
u'rawscore': 7.48625,
u'ref': u'C',
u'segway': u'GM1',
u'sift': {u'cat': u'deleterious', u'val': 0.04},
u'tf': {u'bs': 1, u'bs_peaks': 1, u'bs_peaks_max': 28.018},
u'type': u'SNV'},
u'clinvar': {u'allele_id': 34150,
u'alt': u'T',
u'chrom': u'11',
u'cytogenic': u'11q23.3',
u'gene': {u'id': u'2542', u'symbol': u'SLC37A4'},
u'hg19': {u'end': 118895925, u'start': 118895925},
u'hg38': {u'end': 119025215, u'start': 119025215},
u'hgvs': {u'coding': [u'LRG_187t1:c.1099G>A',
u'NM_001164277.1:c.1099G>A',
u'NM_001467.5:c.1099G>A'],
u'genomic': [u'LRG_187:g.10691G>A',
u'NG_013331.1:g.10691G>A',
u'NC_000011.10:g.119025215C>T',
u'NC_000011.9:g.118895925C>T']},
u'rcv': [{u'accession': u'RCV000020461',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'age_of_onset': u'Neonatal',
u'identifiers': {u'medgen': u'C0268146',
u'omim': u'232220',
u'orphanet': u'79259'},
u'name': u'Glucose-6-phosphate transport defect (GSD1B)',
u'synonyms': [u'GLYCOGEN STORAGE DISEASE Ib', u'GSD Ib']},
u'last_evaluated': u'2010-12-23',
u'number_submitters': 1,
u'origin': u'not provided',
u'preferred_name': u'NM_001164277.1(SLC37A4):c.1099G>A (p.Ala367Thr)',
u'review_status': u'no assertion criteria provided'},
{u'accession': u'RCV000059118',
u'clinical_significance': u'not provided',
u'conditions': {u'identifiers': {u'medgen': u'CN221809'},
u'name': u'not provided'},
u'number_submitters': 1,
u'origin': u'not provided',
u'preferred_name': u'NM_001164277.1(SLC37A4):c.1099G>A (p.Ala367Thr)',
u'review_status': u'no assertion provided'}],
u'ref': u'C',
u'rsid': u'rs80356492',
u'type': u'single nucleotide variant',
u'uniprot': u'VAR_025602',
u'variant_id': 21298},
u'dbnsfp': {u'aa': {u'alt': u'T',
u'codonpos': 1,
u'pos': [u'389', u'294', u'367', u'367'],
u'ref': u'A',
u'refcodon': u'GCC'},
u'alspac': {u'ac': 2, u'af': 0.0005189413596263622},
u'alt': u'T',
u'ancestral_allele': u'C',
u'cds_strand': u'-',
u'chrom': u'11',
u'clinvar': {u'clinsig': 5,
u'rs': u'rs80356492',
u'trait': u'Glucose-6-phosphate_transport_defect'},
u'ensembl': {u'geneid': u'ENSG00000137700',
u'proteinid': [u'ENSP00000476176',
u'ENSP00000475991',
u'ENSP00000475241',
u'ENSP00000476242'],
u'transcriptid': [u'ENST00000357590',
u'ENST00000538950',
u'ENST00000545985',
u'ENST00000330775']},
u'exac': {u'ac': 6,
u'adj_ac': 6,
u'adj_af': 5.226e-05,
u'af': 4.961e-05,
u'afr_ac': 0,
u'afr_af': 0,
u'amr_ac': 0,
u'amr_af': 0,
u'eas_ac': 0,
u'eas_af': 0,
u'fin_ac': 0,
u'fin_af': 0,
u'nfe_ac': 4,
u'nfe_af': 6.276e-05,
u'sas_ac': 2,
u'sas_af': 0.0001281},
u'fathmm-mkl': {u'coding_group': u'AEFDBCIJ',
u'coding_pred': u'D',
u'coding_rankscore': 0.73687,
u'coding_score': 0.97297},
u'genename': u'SLC37A4',
u'gerp++': {u'nr': 5.12, u'rs': 5.12, u'rs_rankscore': 0.69274},
u'gm12878': {u'confidence_value': 0,
u'fitcons_rankscore': 0.04325,
u'fitcons_score': 0.278934},
u'h1-hesc': {u'confidence_value': 0,
u'fitcons_rankscore': 0.04794,
u'fitcons_score': 0.299256},
u'hg18': {u'end': 118401135, u'start': 118401135},
u'hg19': {u'end': 118895925, u'start': 118895925},
u'hg38': {u'end': 119025215, u'start': 119025215},
u'huvec': {u'confidence_value': 0,
u'fitcons_rankscore': 0.03188,
u'fitcons_score': 0.119812},
u'integrated': {u'confidence_value': 0,
u'fitcons_rankscore': 0.04139,
u'fitcons_score': 0.283894},
u'interpro_domain': u'Major facilitator superfamily domain',
u'mutationassessor': {u'pred': u'M', u'rankscore': 0.79762, u'score': 2.47},
u'mutationtaster': {u'converted_rankscore': 0.81033,
u'model': u'without_aae',
u'pred': u'A',
u'score': 1},
u'phastcons': {u'20way': {u'mammalian': 0.971,
u'mammalian_rankscore': 0.46156},
u'7way': {u'vertebrate': 0.996, u'vertebrate_rankscore': 0.63571}},
u'phylo': {u'p20way': {u'mammalian': 0.935,
u'mammalian_rankscore': 0.48811},
u'p7way': {u'vertebrate': 0.871, u'vertebrate_rankscore': 0.44667}},
u'polyphen2': {u'hdiv': {u'pred': u'D',
u'rankscore': 0.76378,
u'score': [0.997, 0.998, 0.999, 0.998]},
u'hvar': {u'pred': u'D',
u'rankscore': 0.69333,
u'score': [0.932, 0.932, 0.964, 0.932]}},
u'ref': u'C',
u'rsid': u'rs80356492',
u'siphy_29way': {u'logodds': 18.3397,
u'logodds_rankscore': 0.90175,
u'pi': {u'a': 0.0, u'c': 1.0, u'g': 0.0, u't': 0.0}},
u'twinsuk': {u'ac': 0, u'af': 0.0},
u'uniprot': [{u'acc': u'B4DPL8', u'pos': u'351'},
{u'acc': u'Q6IBR9', u'pos': u'367'},
{u'acc': u'O43826-2', u'pos': u'389'},
{u'acc': u'O43826', u'pos': u'367'}]},
u'dbsnp': {u'allele_origin': u'germline',
u'alleles': [{u'allele': u'C'}, {u'allele': u'T'}],
u'alt': u'T',
u'chrom': u'11',
u'class': u'SNV',
u'dbsnp_build': 131,
u'flags': [u'ASP',
u'LSD',
u'NSM',
u'PM',
u'PMC',
u'REF',
u'RV',
u'S3D',
u'SLO'],
u'gene': {u'geneid': u'2542', u'symbol': u'SLC37A4'},
u'hg19': {u'end': 118895926, u'start': 118895925},
u'ref': u'C',
u'rsid': u'rs80356492',
u'validated': False,
u'var_subtype': u'ts',
u'vartype': u'snp'},
u'exac': {u'ac': {u'ac': 6,
u'ac_adj': 6,
u'ac_afr': 0,
u'ac_amr': 0,
u'ac_eas': 0,
u'ac_fin': 0,
u'ac_nfe': 4,
u'ac_oth': 0,
u'ac_sas': 2},
u'af': 4.961e-05,
u'alleles': u'T',
u'alt': u'T',
u'an': {u'an': 120950,
u'an_adj': 114810,
u'an_afr': 9306,
u'an_amr': 10742,
u'an_eas': 8246,
u'an_fin': 6308,
u'an_nfe': 63734,
u'an_oth': 856,
u'an_sas': 15618},
u'baseqranksum': 0.598,
u'chrom': u'11',
u'clippingranksum': -0.197,
u'culprit': u'MQ',
u'dp': 1412977,
u'fs': 11.779,
u'het': {u'ac_het': 6,
u'het_afr': 0,
u'het_amr': 0,
u'het_eas': 0,
u'het_fin': 0,
u'het_nfe': 4,
u'het_oth': 0,
u'het_sas': 2},
u'hom': {u'ac_hom': 0,
u'hom_afr': 0,
u'hom_amr': 0,
u'hom_eas': 0,
u'hom_fin': 0,
u'hom_nfe': 0,
u'hom_oth': 0,
u'hom_sas': 0},
u'inbreedingcoeff': 0.0012,
u'mq': {u'mq': 59.06, u'mq0': 0, u'mqranksum': 0.717},
u'ncc': 1385,
u'pos': 118895925,
u'qd': 12.08,
u'qual': 2994.9,
u'readposranksum': 0.237,
u'ref': u'C',
u'type': u'snp',
u'vqslod': -0.7519},
u'mutdb': {u'alt': u'A',
u'chrom': u'11',
u'hg19': {u'end': 118895925, u'start': 118895925},
u'mutpred_score': 0.835,
u'ref': u'G',
u'rsid': None,
u'strand': u'm',
u'uniprot_id': u'VAR_025602'},
u'query': u'RCV000059118',
u'snpeff': {u'ann': [{u'cdna': {u'length': u'2356', u'position': u'1606'},
u'cds': {u'length': u'1356', u'position': u'1165'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001164278.1',
u'feature_type': u'transcript',
u'gene_id': u'SLC37A4',
u'gene_name': u'SLC37A4',
u'hgvs_c': u'c.1165G>A',
u'hgvs_p': u'p.Ala389Thr',
u'protein': {u'length': u'451', u'position': u'389'},
u'putative_impact': u'MODERATE',
u'rank': u'11',
u'total': u'12',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2048', u'position': u'1298'},
u'cds': {u'length': u'1290', u'position': u'1099'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001164280.1',
u'feature_type': u'transcript',
u'gene_id': u'SLC37A4',
u'gene_name': u'SLC37A4',
u'hgvs_c': u'c.1099G>A',
u'hgvs_p': u'p.Ala367Thr',
u'protein': {u'length': u'429', u'position': u'367'},
u'putative_impact': u'MODERATE',
u'rank': u'8',
u'total': u'9',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2606', u'position': u'1856'},
u'cds': {u'length': u'1290', u'position': u'1099'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001164277.1',
u'feature_type': u'transcript',
u'gene_id': u'SLC37A4',
u'gene_name': u'SLC37A4',
u'hgvs_c': u'c.1099G>A',
u'hgvs_p': u'p.Ala367Thr',
u'protein': {u'length': u'429', u'position': u'367'},
u'putative_impact': u'MODERATE',
u'rank': u'10',
u'total': u'11',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2032', u'position': u'1282'},
u'cds': {u'length': u'1071', u'position': u'880'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001164279.1',
u'feature_type': u'transcript',
u'gene_id': u'SLC37A4',
u'gene_name': u'SLC37A4',
u'hgvs_c': u'c.880G>A',
u'hgvs_p': u'p.Ala294Thr',
u'protein': {u'length': u'356', u'position': u'294'},
u'putative_impact': u'MODERATE',
u'rank': u'10',
u'total': u'11',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2102', u'position': u'1352'},
u'cds': {u'length': u'1290', u'position': u'1099'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001467.5',
u'feature_type': u'transcript',
u'gene_id': u'SLC37A4',
u'gene_name': u'SLC37A4',
u'hgvs_c': u'c.1099G>A',
u'hgvs_p': u'p.Ala367Thr',
u'protein': {u'length': u'429', u'position': u'367'},
u'putative_impact': u'MODERATE',
u'rank': u'9',
u'total': u'10',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'1540',
u'effect': u'downstream_gene_variant',
u'feature_id': u'NM_016146.4',
u'feature_type': u'transcript',
u'gene_id': u'TRAPPC4',
u'gene_name': u'TRAPPC4',
u'hgvs_c': u'c.*925C>T',
u'putative_impact': u'MODIFIER',
u'transcript_biotype': u'Coding'}]},
u'vcf': {u'alt': u'T', u'position': u'118895925', u'ref': u'C'}},
{u'_id': u'chr11:g.118895906G>T',
u'_score': 16.533304,
u'cadd': {u'_license': u'http://goo.gl/bkpNhq',
u'alt': u'T',
u'anc': u'G',
u'annotype': u'CodingTranscript',
u'bstatistic': 476,
u'chmm': {u'bivflnk': 0.0,
u'enh': 0.197,
u'enhbiv': 0.0,
u'het': 0.0,
u'quies': 0.0,
u'reprpc': 0.0,
u'reprpcwk': 0.0,
u'tssa': 0.0,
u'tssaflnk': 0.0,
u'tssbiv': 0.0,
u'tx': 0.622,
u'txflnk': 0.055,
u'txwk': 0.11,
u'znfrpts': 0.0},
u'chrom': 11,
u'consdetail': u'missense',
u'consequence': u'NON_SYNONYMOUS',
u'consscore': 7,
u'cpg': 0.03,
u'dna': {u'helt': 1.31, u'mgw': 0.37, u'prot': -0.6, u'roll': 5.46},
u'dst2splice': 6,
u'dst2spltype': u'DONOR',
u'encode': {u'exp': 125.32,
u'h3k27ac': 13.84,
u'h3k4me1': 33.84,
u'h3k4me3': 6.4,
u'nucleo': 2.1,
u'occ': 2,
u'p_val': {u'comb': 0.95,
u'ctcf': 0.0,
u'dnas': 1.62,
u'faire': 0.0,
u'mycp': 0.0,
u'polii': 0.0},
u'sig': {u'ctcf': 0.03,
u'dnase': 0.04,
u'faire': 0.01,
u'myc': 0.0,
u'polii': 0.0}},
u'exon': u'11/12',
u'fitcons': 0.2838,
u'gc': 0.53,
u'gene': {u'cds': {u'cdna_pos': 1625,
u'cds_pos': 1184,
u'rel_cdna_pos': 0.69,
u'rel_cds_pos': 0.87},
u'feature_id': u'ENST00000357590',
u'gene_id': u'ENSG00000137700',
u'genename': u'SLC37A4',
u'prot': {u'domain': u'tmhmm', u'protpos': 395, u'rel_prot_pos': 0.88}},
u'gerp': {u'n': 5.27, u'rs': 2485.2, u'rs_pval': 2.73146e-114, u's': 5.27},
u'grantham': 126,
u'isderived': u'TRUE',
u'isknownvariant': u'FALSE',
u'istv': u'TRUE',
u'length': 0,
u'mapability': {u'20bp': 1, u'35bp': 1},
u'min_dist_tse': 44,
u'min_dist_tss': 3839,
u'mutindex': 35,
u'naa': u'D',
u'oaa': u'A',
u'phast_cons': {u'mammalian': 1.0, u'primate': 0.989, u'vertebrate': 1.0},
u'phred': 33,
u'phylop': {u'mammalian': 2.754, u'primate': 0.557, u'vertebrate': 5.928},
u'polyphen': {u'cat': u'probably_damaging', u'val': 0.956},
u'pos': 118895906,
u'rawscore': 6.879844,
u'ref': u'G',
u'segway': u'GM1',
u'sift': {u'cat': u'deleterious', u'val': 0},
u'tf': {u'bs': 1, u'bs_peaks': 1, u'bs_peaks_max': 28.018},
u'type': u'SNV'},
u'clinvar': {u'allele_id': 79160,
u'alt': u'T',
u'chrom': u'11',
u'cytogenic': u'11q23.3',
u'gene': {u'id': u'2542', u'symbol': u'SLC37A4'},
u'hg19': {u'end': 118895906, u'start': 118895906},
u'hg38': {u'end': 119025196, u'start': 119025196},
u'hgvs': {u'coding': [u'LRG_187t1:c.1118C>A', u'NM_001164277.1:c.1118C>A'],
u'genomic': [u'LRG_187:g.10710C>A',
u'NG_013331.1:g.10710C>A',
u'NC_000011.10:g.119025196G>T',
u'NC_000011.9:g.118895906G>T']},
u'rcv': {u'accession': u'RCV000059119',
u'clinical_significance': u'not provided',
u'conditions': {u'identifiers': {u'medgen': u'CN221809'},
u'name': u'not provided'},
u'number_submitters': 1,
u'origin': u'not provided',
u'preferred_name': u'NM_001164277.1(SLC37A4):c.1118C>A (p.Ala373Asp)',
u'review_status': u'no assertion provided'},
u'ref': u'G',
u'rsid': u'rs193302901',
u'type': u'single nucleotide variant',
u'uniprot': u'VAR_025603',
u'variant_id': 68269},
u'dbnsfp': {u'aa': {u'alt': u'D',
u'codonpos': 2,
u'pos': [u'395', u'300', u'373', u'373'],
u'ref': u'A',
u'refcodon': u'GCC'},
u'alt': u'T',
u'ancestral_allele': u'G',
u'cds_strand': u'-',
u'chrom': u'11',
u'ensembl': {u'geneid': u'ENSG00000137700',
u'proteinid': [u'ENSP00000476176',
u'ENSP00000475991',
u'ENSP00000475241',
u'ENSP00000476242'],
u'transcriptid': [u'ENST00000357590',
u'ENST00000538950',
u'ENST00000545985',
u'ENST00000330775']},
u'fathmm-mkl': {u'coding_group': u'AEFDBCIJ',
u'coding_pred': u'D',
u'coding_rankscore': 0.70831,
u'coding_score': 0.96804},
u'genename': u'SLC37A4',
u'gerp++': {u'nr': 5.27, u'rs': 5.27, u'rs_rankscore': 0.73637},
u'gm12878': {u'confidence_value': 0,
u'fitcons_rankscore': 0.04325,
u'fitcons_score': 0.278934},
u'h1-hesc': {u'confidence_value': 0,
u'fitcons_rankscore': 0.04794,
u'fitcons_score': 0.299256},
u'hg18': {u'end': 118401116, u'start': 118401116},
u'hg19': {u'end': 118895906, u'start': 118895906},
u'hg38': {u'end': 119025196, u'start': 119025196},
u'huvec': {u'confidence_value': 0,
u'fitcons_rankscore': 0.03188,
u'fitcons_score': 0.119812},
u'integrated': {u'confidence_value': 0,
u'fitcons_rankscore': 0.04139,
u'fitcons_score': 0.283894},
u'interpro_domain': u'Major facilitator superfamily domain',
u'mutationassessor': {u'pred': u'M',
u'rankscore': 0.89652,
u'score': 3.055},
u'mutationtaster': {u'converted_rankscore': 0.81033,
u'model': u'without_aae',
u'pred': u'D',
u'score': 1},
u'phastcons': {u'20way': {u'mammalian': 1.0,
u'mammalian_rankscore': 0.88722},
u'7way': {u'vertebrate': 1.0, u'vertebrate_rankscore': 0.90892}},
u'phylo': {u'p20way': {u'mammalian': 1.048,
u'mammalian_rankscore': 0.71188},
u'p7way': {u'vertebrate': 0.917, u'vertebrate_rankscore': 0.60462}},
u'polyphen2': {u'hdiv': {u'pred': u'D',
u'rankscore': 0.64686,
u'score': [0.994, 0.989, 0.993, 0.989]},
u'hvar': {u'pred': u'D',
u'rankscore': 0.71516,
u'score': [0.965, 0.965, 0.956, 0.974]}},
u'ref': u'G',
u'rsid': u'rs193302901',
u'siphy_29way': {u'logodds': 18.6812,
u'logodds_rankscore': 0.91448,
u'pi': {u'a': 0.0, u'c': 0.0, u'g': 1.0, u't': 0.0}},
u'uniprot': [{u'acc': u'B4DPL8', u'pos': u'357'},
{u'acc': u'Q6IBR9', u'pos': u'373'},
{u'acc': u'O43826-2', u'pos': u'395'},
{u'acc': u'O43826', u'pos': u'373'}]},
u'dbsnp': {u'allele_origin': u'unspecified',
u'alleles': [{u'allele': u'G'}, {u'allele': u'C'}, {u'allele': u'T'}],
u'alt': u'T',
u'chrom': u'11',
u'class': u'SNV',
u'dbsnp_build': 135,
u'flags': [u'ASP',
u'LSD',
u'NSM',
u'PM',
u'PMC',
u'REF',
u'RV',
u'S3D',
u'SLO'],
u'gene': {u'geneid': u'2542', u'symbol': u'SLC37A4'},
u'hg19': {u'end': 118895907, u'start': 118895906},
u'ref': u'G',
u'rsid': u'rs193302901',
u'validated': False,
u'var_subtype': u'unknown',
u'vartype': u'snp'},
u'mutdb': {u'alt': u'A',
u'chrom': u'11',
u'hg19': {u'end': 118895906, u'start': 118895906},
u'mutpred_score': 0.82,
u'ref': u'C',
u'rsid': None,
u'strand': u'm',
u'uniprot_id': u'VAR_025603'},
u'query': u'RCV000059119',
u'snpeff': {u'ann': [{u'cdna': {u'length': u'2356', u'position': u'1625'},
u'cds': {u'length': u'1356', u'position': u'1184'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001164278.1',
u'feature_type': u'transcript',
u'gene_id': u'SLC37A4',
u'gene_name': u'SLC37A4',
u'hgvs_c': u'c.1184C>A',
u'hgvs_p': u'p.Ala395Asp',
u'protein': {u'length': u'451', u'position': u'395'},
u'putative_impact': u'MODERATE',
u'rank': u'11',
u'total': u'12',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2048', u'position': u'1317'},
u'cds': {u'length': u'1290', u'position': u'1118'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001164280.1',
u'feature_type': u'transcript',
u'gene_id': u'SLC37A4',
u'gene_name': u'SLC37A4',
u'hgvs_c': u'c.1118C>A',
u'hgvs_p': u'p.Ala373Asp',
u'protein': {u'length': u'429', u'position': u'373'},
u'putative_impact': u'MODERATE',
u'rank': u'8',
u'total': u'9',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2606', u'position': u'1875'},
u'cds': {u'length': u'1290', u'position': u'1118'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001164277.1',
u'feature_type': u'transcript',
u'gene_id': u'SLC37A4',
u'gene_name': u'SLC37A4',
u'hgvs_c': u'c.1118C>A',
u'hgvs_p': u'p.Ala373Asp',
u'protein': {u'length': u'429', u'position': u'373'},
u'putative_impact': u'MODERATE',
u'rank': u'10',
u'total': u'11',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2032', u'position': u'1301'},
u'cds': {u'length': u'1071', u'position': u'899'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001164279.1',
u'feature_type': u'transcript',
u'gene_id': u'SLC37A4',
u'gene_name': u'SLC37A4',
u'hgvs_c': u'c.899C>A',
u'hgvs_p': u'p.Ala300Asp',
u'protein': {u'length': u'356', u'position': u'300'},
u'putative_impact': u'MODERATE',
u'rank': u'10',
u'total': u'11',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2102', u'position': u'1371'},
u'cds': {u'length': u'1290', u'position': u'1118'},
u'effect': u'missense_variant',
u'feature_id': u'NM_001467.5',
u'feature_type': u'transcript',
u'gene_id': u'SLC37A4',
u'gene_name': u'SLC37A4',
u'hgvs_c': u'c.1118C>A',
u'hgvs_p': u'p.Ala373Asp',
u'protein': {u'length': u'429', u'position': u'373'},
u'putative_impact': u'MODERATE',
u'rank': u'9',
u'total': u'10',
u'transcript_biotype': u'Coding'},
{u'distance_to_feature': u'1521',
u'effect': u'downstream_gene_variant',
u'feature_id': u'NM_016146.4',
u'feature_type': u'transcript',
u'gene_id': u'TRAPPC4',
u'gene_name': u'TRAPPC4',
u'hgvs_c': u'c.*925G>T',
u'putative_impact': u'MODIFIER',
u'transcript_biotype': u'Coding'}]},
u'vcf': {u'alt': u'T', u'position': u'118895906', u'ref': u'G'}},
{u'_id': u'chr1:g.156105869_156105869del',
u'_score': 16.53367,
u'clinvar': {u'allele_id': 77674,
u'alt': u'-',
u'chrom': u'1',
u'cytogenic': u'1q22',
u'gene': {u'id': u'4000', u'symbol': u'LMNA'},
u'hg19': {u'end': 156105869, u'start': 156105869},
u'hg38': {u'end': 156136078, u'start': 156136078},
u'hgvs': {u'coding': [u'LRG_254t1:c.1114delG',
u'NM_005572.3:c.1114delG',
u'NM_170707.3:c.1114delG',
u'NM_170708.3:c.1114delG'],
u'genomic': [u'LRG_254:g.58506delG',
u'NG_008692.2:g.58506delG',
u'NC_000001.11:g.156136078delG',
u'NC_000001.10:g.156105869delG']},
u'rcv': {u'accession': u'RCV000057234',
u'clinical_significance': u'not provided',
u'conditions': {u'identifiers': {u'medgen': u'CN221809'},
u'name': u'not provided'},
u'number_submitters': 1,
u'origin': u'not provided',
u'preferred_name': u'NM_005572.3(LMNA):c.1114delG (p.Glu372Argfs)',
u'review_status': u'no assertion provided'},
u'ref': u'G',
u'rsid': u'rs267607575',
u'type': u'Deletion',
u'variant_id': 66777},
u'query': u'RCV000057234',
u'snpeff': {u'ann': [{u'cdna': {u'length': u'3227', u'position': u'1363'},
u'cds': {u'length': u'1995', u'position': u'1114'},
u'effect': u'frameshift_variant',
u'feature_id': u'NM_170707.3',
u'feature_type': u'transcript',
u'gene_id': u'LMNA',
u'gene_name': u'LMNA',
u'hgvs_c': u'c.1114delG',
u'hgvs_p': u'p.Glu372fs',
u'protein': {u'length': u'664', u'position': u'372'},
u'putative_impact': u'HIGH',
u'rank': u'6',
u'total': u'12',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2494', u'position': u'1787'},
u'cds': {u'length': u'1719', u'position': u'1114'},
u'effect': u'frameshift_variant',
u'feature_id': u'NM_001282625.1',
u'feature_type': u'transcript',
u'gene_id': u'LMNA',
u'gene_name': u'LMNA',
u'hgvs_c': u'c.1114delG',
u'hgvs_p': u'p.Glu372fs',
u'protein': {u'length': u'572', u'position': u'372'},
u'putative_impact': u'HIGH',
u'rank': u'9',
u'total': u'13',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2070', u'position': u'1363'},
u'cds': {u'length': u'1719', u'position': u'1114'},
u'effect': u'frameshift_variant',
u'feature_id': u'NM_005572.3',
u'feature_type': u'transcript',
u'gene_id': u'LMNA',
u'gene_name': u'LMNA',
u'hgvs_c': u'c.1114delG',
u'hgvs_p': u'p.Glu372fs',
u'protein': {u'length': u'572', u'position': u'372'},
u'putative_impact': u'HIGH',
u'rank': u'6',
u'total': u'10',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'3077', u'position': u'1363'},
u'cds': {u'length': u'1845', u'position': u'1114'},
u'effect': u'frameshift_variant',
u'feature_id': u'NM_001282626.1',
u'feature_type': u'transcript',
u'gene_id': u'LMNA',
u'gene_name': u'LMNA',
u'hgvs_c': u'c.1114delG',
u'hgvs_p': u'p.Glu372fs',
u'protein': {u'length': u'614', u'position': u'372'},
u'putative_impact': u'HIGH',
u'rank': u'6',
u'total': u'12',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'3137', u'position': u'1363'},
u'cds': {u'length': u'1905', u'position': u'1114'},
u'effect': u'frameshift_variant',
u'feature_id': u'NM_170708.3',
u'feature_type': u'transcript',
u'gene_id': u'LMNA',
u'gene_name': u'LMNA',
u'hgvs_c': u'c.1114delG',
u'hgvs_p': u'p.Glu372fs',
u'protein': {u'length': u'634', u'position': u'372'},
u'putative_impact': u'HIGH',
u'rank': u'6',
u'total': u'11',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'1752', u'position': u'1045'},
u'cds': {u'length': u'1476', u'position': u'871'},
u'effect': u'frameshift_variant',
u'feature_id': u'NM_001282624.1',
u'feature_type': u'transcript',
u'gene_id': u'LMNA',
u'gene_name': u'LMNA',
u'hgvs_c': u'c.871delG',
u'hgvs_p': u'p.Glu291fs',
u'protein': {u'length': u'491', u'position': u'291'},
u'putative_impact': u'HIGH',
u'rank': u'7',
u'total': u'11',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2062', u'position': u'865'},
u'cds': {u'length': u'1725', u'position': u'778'},
u'effect': u'frameshift_variant',
u'feature_id': u'NM_001257374.2',
u'feature_type': u'transcript',
u'gene_id': u'LMNA',
u'gene_name': u'LMNA',
u'hgvs_c': u'c.778delG',
u'hgvs_p': u'p.Glu260fs',
u'protein': {u'length': u'574', u'position': u'260'},
u'putative_impact': u'HIGH',
u'rank': u'6',
u'total': u'13',
u'transcript_biotype': u'Coding'},
{u'effect': u'intron_variant',
u'feature_id': u'NR_107005.1',
u'feature_type': u'transcript',
u'gene_id': u'MIR7851',
u'gene_name': u'MIR7851',
u'hgvs_c': u'n.43+23752delC',
u'putative_impact': u'MODIFIER',
u'rank': u'3',
u'total': u'4',
u'transcript_biotype': u'Noncoding'}],
u'lof': {u'gene_id': u'LMNA',
u'gene_name': u'LMNA',
u'number_of_transcripts_in_gene': u'7',
u'percent_of_transcripts_affected': u'1.00'}},
u'vcf': {u'alt': u'G', u'position': u'156105868', u'ref': u'GG'}},
{u'_id': u'chr14:g.23874929G>A',
u'_score': 16.533554,
u'cadd': {u'_license': u'http://goo.gl/bkpNhq',
u'alt': u'A',
u'anc': u'G',
u'annotype': u'CodingTranscript',
u'bstatistic': 653,
u'chmm': {u'bivflnk': 0.0,
u'enh': 0.008,
u'enhbiv': 0.008,
u'het': 0.008,
u'quies': 0.339,
u'reprpc': 0.189,
u'reprpcwk': 0.394,
u'tssa': 0.008,
u'tssaflnk': 0.0,
u'tssbiv': 0.0,
u'tx': 0.008,
u'txflnk': 0.016,
u'txwk': 0.008,
u'znfrpts': 0.0},
u'chrom': 14,
u'consdetail': u'synonymous',
u'consequence': u'SYNONYMOUS',
u'consscore': 5,
u'cpg': 0.09,
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u'nucleo': 2.0,
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u'mycp': 0.0,
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u'exon': u'4/39',
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u'cds': {u'cdna_pos': 323,
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u'rel_cds_pos': 0.04},
u'feature_id': u'ENST00000405093',
u'gene_id': u'ENSG00000197616',
u'genename': u'MYH6',
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u'gerp': {u'n': 3.91, u'rs': 442.1, u'rs_pval': 2.08598e-40, u's': 3.91},
u'isderived': u'TRUE',
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u'mapability': {u'20bp': 0.5, u'35bp': 1},
u'min_dist_tse': 6008,
u'min_dist_tss': 1873,
u'mutindex': 76,
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u'phast_cons': {u'mammalian': 1.0, u'primate': 0.997, u'vertebrate': 1.0},
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u'clinvar': {u'allele_id': 53632,
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u'chrom': u'14',
u'cytogenic': u'14q11.2',
u'gene': {u'id': u'4624', u'symbol': u'MYH6'},
u'hg19': {u'end': 23874929, u'start': 23874929},
u'hg38': {u'end': 23405720, u'start': 23405720},
u'hgvs': {u'coding': [u'LRG_389t1:c.252C>T', u'NM_002471.3:c.252C>T'],
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u'NC_000014.8:g.23874929G>A']},
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u'rsid': u'rs397516757',
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u'hg19': {u'end': 23874930, u'start': 23874929},
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u'var_subtype': u'ts',
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u'feature_type': u'transcript',
u'gene_id': u'MYH6',
u'gene_name': u'MYH6',
u'hgvs_c': u'c.252C>T',
u'hgvs_p': u'p.Phe84Phe',
u'protein': {u'length': u'1939', u'position': u'84'},
u'putative_impact': u'LOW',
u'rank': u'4',
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u'transcript_biotype': u'Coding'}},
u'vcf': {u'alt': u'A', u'position': u'23874929', u'ref': u'G'}},
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u'cadd': {u'1000g': {u'af': 0.02, u'afr': 0.004, u'amr': 0.02, u'eur': 0.05},
u'_license': u'http://goo.gl/bkpNhq',
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u'anc': u'G',
u'annotype': u'CodingTranscript',
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u'rel_cds_pos': 0.81},
u'feature_id': u'ENST00000357618',
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u'grantham': 194,
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u'polyphen': {u'cat': u'probably_damaging', u'val': 0.915},
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u'rawscore': 5.269899,
u'ref': u'G',
u'segway': u'GM1',
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u'clinvar': {u'allele_id': 15048,
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u'chrom': u'6',
u'cytogenic': u'6p22.2',
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u'hg38': {u'end': 26092913, u'start': 26092913},
u'hgvs': {u'coding': [u'LRG_748t1:c.845G>A',
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u'genomic': [u'LRG_748:g.10633G>A',
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u'omim': u'613609.0001',
u'rcv': [{u'accession': u'RCV000000019',
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u'omim': u'235200'},
u'name': u'Hemochromatosis type 1 (HFE1)'},
u'last_evaluated': u'2015-09-17',
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u'origin': u'germline',
u'preferred_name': u'NM_000410.3(HFE):c.845G>A (p.Cys282Tyr)',
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u'preferred_name': u'NM_000410.3(HFE):c.845G>A (p.Cys282Tyr)',
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{u'accession': u'RCV000000021',
u'clinical_significance': u'risk factor',
u'conditions': {u'name': u'Porphyria variegata, susceptibility to'},
u'last_evaluated': u'2009-01-01',
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u'origin': u'germline',
u'preferred_name': u'NM_000410.3(HFE):c.845G>A (p.Cys282Tyr)',
u'review_status': u'no assertion criteria provided'},
{u'accession': u'RCV000000022',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'name': u'Hemochromatosis, juvenile, digenic'},
u'last_evaluated': u'2009-01-01',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_000410.3(HFE):c.845G>A (p.Cys282Tyr)',
u'review_status': u'no assertion criteria provided'},
{u'accession': u'RCV000000023',
u'clinical_significance': u'risk factor',
u'conditions': {u'name': u'Alzheimer disease, susceptibility to'},
u'last_evaluated': u'2009-01-01',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_000410.3(HFE):c.845G>A (p.Cys282Tyr)',
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{u'accession': u'RCV000000024',
u'clinical_significance': u'association',
u'conditions': {u'identifiers': {u'medgen': u'C3280096',
u'omim': u'614193'},
u'name': u'Transferrin serum level quantitative trait locus 2 (TFQTL2)'},
u'last_evaluated': u'2009-01-01',
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u'origin': u'germline',
u'preferred_name': u'NM_000410.3(HFE):c.845G>A (p.Cys282Tyr)',
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{u'accession': u'RCV000000025',
u'clinical_significance': u'risk factor',
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u'name': u'Microvascular complications of diabetes 7 (MVCD7)',
u'synonyms': [u'MICROVASCULAR COMPLICATIONS OF DIABETES, SUSCEPTIBILITY TO, 7',
u'NEPHROPATHY, DIABETIC, SUSCEPTIBILITY TO',
u'NONPROLIFERATIVE RETINOPATHY, DIABETIC, SUSCEPTIBILITY TO',
u'PROLIFERATIVE RETINOPATHY, DIABETIC, SUSCEPTIBILITY TO']},
u'last_evaluated': u'2009-01-01',
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u'origin': u'germline',
u'preferred_name': u'NM_000410.3(HFE):c.845G>A (p.Cys282Tyr)',
u'review_status': u'no assertion criteria provided'},
{u'accession': u'RCV000117222',
u'clinical_significance': u'Benign',
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u'name': u'not specified',
u'synonyms': u'AllHighlyPenetrant'},
u'last_evaluated': u'2013-11-04',
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u'origin': u'germline',
u'preferred_name': u'NM_000410.3(HFE):c.845G>A (p.Cys282Tyr)',
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{u'accession': u'RCV000178096',
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u'name': u'not provided'},
u'last_evaluated': u'2014-10-13',
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u'origin': u'germline',
u'preferred_name': u'NM_000410.3(HFE):c.845G>A (p.Cys282Tyr)',
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u'rsid': u'rs1800562',
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u'dbnsfp': {u'1000gp3': {u'ac': 63,
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u'afr_ac': 3,
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u'eas_ac': 0,
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u'190',
u'282',
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u'176',
u'268',
u'180',
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u'refcodon': u'TGC'},
u'alspac': {u'ac': 306, u'af': 0.07939802802283343},
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u'ancestral_allele': u'G',
u'cds_strand': u'+',
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u'clinvar': {u'clinsig': 5,
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u'trait': u'Hereditary_hemochromatosis|Hemochromatosis\\x2c_juvenile\\x2c_digenic|not_specified'},
u'ensembl': {u'geneid': u'ENSG00000010704',
u'proteinid': [u'ENSP00000380217',
u'ENSP00000312342',
u'ENSP00000259699',
u'ENSP00000313776',
u'ENSP00000417404',
u'ENSP00000419725',
u'ENSP00000337819',
u'ENSP00000420802',
u'ENSP00000420559',
u'ENSP00000311698'],
u'transcriptid': [u'ENST00000397022',
u'ENST00000353147',
u'ENST00000349999',
u'ENST00000317896',
u'ENST00000357618',
u'ENST00000470149',
u'ENST00000336625',
u'ENST00000461397',
u'ENST00000488199',
u'ENST00000309234']},
u'esp6500': {u'aa_ac': 67,
u'aa_af': 0.015206536541080345,
u'ea_ac': 551,
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u'exac': {u'ac': 3937,
u'adj_ac': 3937,
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u'afr_ac': 105,
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u'amr_ac': 133,
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u'eas_ac': 1,
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u'fathmm': {u'pred': [u'D',
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u'D',
u'D',
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u'score': [-3.68,
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u'fathmm-mkl': {u'coding_group': u'AEFDBI',
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u'gerp++': {u'nr': 5.35, u'rs': 5.35, u'rs_rankscore': 0.76149},
u'gm12878': {u'confidence_value': 0,
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u'fitcons_score': 0.624146},
u'h1-hesc': {u'confidence_value': 0,
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u'fitcons_score': 0.602189},
u'hg18': {u'end': 26201120, u'start': 26201120},
u'hg19': {u'end': 26093141, u'start': 26093141},
u'hg38': {u'end': 26092913, u'start': 26092913},
u'huvec': {u'confidence_value': 0,
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u'fitcons_score': 0.579976},
u'integrated': {u'confidence_value': 0,
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u'fitcons_score': 0.623552},
u'interpro_domain': [u'Immunoglobulin C1-set',
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u'Immunoglobulin-like fold',
u'Immunoglobulin/major histocompatibility complex, conserved site',
u'MHC class I alpha chain, alpha1 alpha2 domains',
u'MHC class I-like antigen recognition',
u'MHC classes I/II-like antigen recognition protein'],
u'lrt': {u'converted_rankscore': 0.62918,
u'omega': 0.0,
u'pred': u'D',
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u'metalr': {u'pred': u'D', u'rankscore': 0.98433, u'score': 0.9518},
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u'mutationassessor': {u'pred': u'H',
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u'score': 4.445},
u'mutationtaster': {u'AAE': [u'C180Y',
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u'C102Y',
u'C268Y',
u'C190Y',
u'C259Y',
u'C176Y',
u'C282Y',
u'C279Y',
u'C282Y',
u'.'],
u'converted_rankscore': 0.81033,
u'model': [u'simple_aae',
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u'A',
u'A',
u'A',
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u'score': [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]},
u'phastcons': {u'20way': {u'mammalian': 0.895,
u'mammalian_rankscore': 0.37584},
u'7way': {u'vertebrate': 0.669, u'vertebrate_rankscore': 0.28987}},
u'phylo': {u'p20way': {u'mammalian': 1.048,
u'mammalian_rankscore': 0.71188},
u'p7way': {u'vertebrate': 0.917, u'vertebrate_rankscore': 0.60462}},
u'polyphen2': {u'hdiv': {u'pred': [u'D',
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u'score': [0.982, 1.0, 1.0, 1.0, 1.0, 0.951, 0.996, 0.993, 0.961]},
u'hvar': {u'pred': [u'P', u'D', u'D', u'D', u'D', u'P', u'P', u'D', u'P'],
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u'score': [0.756,
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u'provean': {u'pred': u'D',
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u'ref': u'G',
u'reliability_index': 9,
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u'pi': {u'a': 0.0, u'c': 0.0, u'g': 1.0, u't': 0.0}},
u'twinsuk': {u'ac': 256, u'af': 0.06903991370010787},
u'uniprot': [{u'acc': u'Q6B0J5', u'pos': u'279'},
{u'acc': u'Q30201-6', u'pos': u'102'},
{u'acc': u'Q30201-4', u'pos': u'180'},
{u'acc': u'Q30201-7', u'pos': u'190'},
{u'acc': u'Q30201-10', u'pos': u'176'},
{u'acc': u'Q30201-3', u'pos': u'268'},
{u'acc': u'Q30201-2', u'pos': u'194'},
{u'acc': u'Q30201-5', u'pos': u'259'},
{u'acc': u'Q30201', u'pos': u'282'}]},
u'dbsnp': {u'allele_origin': u'germline',
u'alleles': [{u'allele': u'G', u'freq': 0.9874},
{u'allele': u'A', u'freq': 0.01258}],
u'alt': u'A',
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u'dbsnp_build': 89,
u'flags': [u'ASP',
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u'INT',
u'KGPhase1',
u'KGPhase3',
u'LSD',
u'MTP',
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u'REF',
u'S3D',
u'SLO'],
u'gene': {u'geneid': u'3077', u'symbol': u'HFE'},
u'gmaf': 0.01258,
u'hg19': {u'end': 26093142, u'start': 26093141},
u'ref': u'G',
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u'validated': True,
u'var_subtype': u'ts',
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u'evs': {u'allele_count': {u'african_american': {u'A': 67, u'G': 4339},
u'all': {u'A': 618, u'G': 12388},
u'european_american': {u'A': 551, u'G': 8049}},
u'alt': u'A',
u'avg_sample_read': 82,
u'chimp_allele': u'G',
u'chrom': 6,
u'clinical_info': u'http://www.ncbi.nlm.nih.gov/sites/varvu?gene=3077&rs=1800562|http://www.ncbi.nlm.nih.gov/omim/235200,235200|http://omim.org/entry/613609#0001|http://omim.org/entry/235200#0001|http://www.ncbi.nlm.nih.gov/pubmed?term=19084217,19820697,19820699,19862010,20686565,20858683,20927387,21665994,21785125,21943158,23263863',
u'coding_dna_size': [231, 507, 978, 741, 783, 1005, 771, 729, 1047],
u'conservation': {u'gerp': 5.3, u'phast_cons': 1.0},
u'dbsnp_version': 89,
u'filter_status': u'PASS',
u'function_gvs': [u'intron',
u'missense',
u'missense',
u'missense',
u'missense',
u'missense',
u'missense',
u'missense',
u'missense'],
u'gene': [{u'accession': u'NM_139011.2', u'symbol': u'HFE'},
{u'accession': u'NM_139010.2', u'symbol': u'HFE'},
{u'accession': u'NM_139009.2', u'symbol': u'HFE'},
{u'accession': u'NM_139008.2', u'symbol': u'HFE'},
{u'accession': u'NM_139007.2', u'symbol': u'HFE'},
{u'accession': u'NM_139006.2', u'symbol': u'HFE'},
{u'accession': u'NM_139004.2', u'symbol': u'HFE'},
{u'accession': u'NM_139003.2', u'symbol': u'HFE'},
{u'accession': u'NM_000410.3', u'symbol': u'HFE'}],
u'genotype_count': {u'african_american': {u'AA': 1, u'AG': 65, u'GG': 2137},
u'all_genotype': {u'AA': 19, u'AG': 580, u'GG': 5904},
u'european_american': {u'AA': 18, u'AG': 515, u'GG': 3767}},
u'gwas_pubmed_info': u'http://www.ncbi.nlm.nih.gov/pubmed?term=19084217,19820697,19820699,19862010,20686565,20858683,20927387,21483845,21665994,21785125,21943158,23263863',
u'hg19': {u'end': 26093141, u'start': 26093141},
u'hg38': {u'end': 26092913, u'start': 26092913},
u'hgvs': [{u'coding': u'c.77-206G>A'},
{u'coding': u'c.305G>A', u'protein': u'p.(C102Y)'},
{u'coding': u'c.776G>A', u'protein': u'p.(C259Y)'},
{u'coding': u'c.539G>A', u'protein': u'p.(C180Y)'},
{u'coding': u'c.581G>A', u'protein': u'p.(C194Y)'},
{u'coding': u'c.803G>A', u'protein': u'p.(C268Y)'},
{u'coding': u'c.569G>A', u'protein': u'p.(C190Y)'},
{u'coding': u'c.527G>A', u'protein': u'p.(C176Y)'},
{u'coding': u'c.845G>A', u'protein': u'p.(C282Y)'}],
u'ma_fin_percent': {u'african_american': 1.5207,
u'all': 4.7517,
u'european_american': 6.407},
u'on_illumina_human_exome_chip': u'yes',
u'polyphen2': [{u'class': u'u', u'score': u'n'},
{u'class': u'p', u'score': u'r'},
{u'class': u'p', u'score': u'r'},
{u'class': u'p', u'score': u'r'},
{u'class': u'p', u'score': u'r'},
{u'class': u'p', u'score': u'r'},
{u'class': u'p', u'score': u'r'},
{u'class': u'p', u'score': u'r'},
{u'class': u'p', u'score': u'r'}],
u'ref': u'G',
u'ref_base_ncbi': u'G',
u'rsid': u'rs1800562'},
u'exac': {u'ac': {u'ac': 3937,
u'ac_adj': 3937,
u'ac_afr': 105,
u'ac_amr': 133,
u'ac_eas': 1,
u'ac_fin': 213,
u'ac_nfe': 3427,
u'ac_oth': 20,
u'ac_sas': 38},
u'af': 0.032,
u'alleles': u'A',
u'alt': u'A',
u'an': {u'an': 121412,
u'an_adj': 121394,
u'an_afr': 10406,
u'an_amr': 11572,
u'an_eas': 8654,
u'an_fin': 6608,
u'an_nfe': 66734,
u'an_oth': 908,
u'an_sas': 16512},
u'baseqranksum': -3.408,
u'chrom': u'6',
u'clippingranksum': -0.301,
u'culprit': u'FS',
u'dp': 1947210,
u'fs': 0.0,
u'het': {u'ac_het': 3697,
u'het_afr': 103,
u'het_amr': 129,
u'het_eas': 1,
u'het_fin': 199,
u'het_nfe': 3209,
u'het_oth': 18,
u'het_sas': 38},
u'hom': {u'ac_hom': 120,
u'hom_afr': 1,
u'hom_amr': 2,
u'hom_eas': 0,
u'hom_fin': 7,
u'hom_nfe': 109,
u'hom_oth': 1,
u'hom_sas': 0},
u'inbreedingcoeff': 0.0198,
u'mq': {u'mq': 59.63, u'mq0': 0, u'mqranksum': 0.137},
u'ncc': 1,
u'pos': 26093141,
u'qd': 12.8,
u'qual': 6196720.01,
u'readposranksum': 0.46,
u'ref': u'G',
u'type': u'snp',
u'vqslod': 6.81},
u'grasp': {u'creation_date': u'8/17/12',
u'discovery': [{u'european': 19840, u'total_samples': 19840},
{u'european': 459, u'total_samples': 459},
{u'european': 459, u'total_samples': 459},
{u'european': 459, u'total_samples': 459},
{u'european': 459, u'total_samples': 459},
{u'european': 4627, u'total_samples': 4627},
{u'european': 4627, u'total_samples': 4627},
{u'european': 4627, u'total_samples': 4627},
{u'european': 4627, u'total_samples': 4627},
{u'european': 4627, u'total_samples': 4627},
{u'european': 4818, u'total_samples': 4818},
{u'european': 4818, u'total_samples': 4818},
{u'european': 4818, u'total_samples': 4818},
{u'european': 4818, u'total_samples': 4818},
{u'european': 4818, u'total_samples': 4818},
{u'european': 4818, u'total_samples': 4818},
{u'european': 24167, u'total_samples': 24167},
{u'european': 24167, u'total_samples': 24167},
{u'european': 24167, u'total_samples': 24167},
{u'european': 24167, u'total_samples': 24167},
{u'european': 24167, u'total_samples': 24167},
{u'european': 67093, u'total_samples': 67093},
{u'european': 100184, u'total_samples': 100184},
{u'european': 100184, u'total_samples': 100184},
{u'european': 46368, u'total_samples': 46368},
{u'european': 46368, u'total_samples': 46368},
{u'european': 46368, u'total_samples': 46368},
{u'european': 46368, u'total_samples': 46368},
{u'european': 46368, u'total_samples': 46368},
{u'european': 46368, u'total_samples': 46368},
{u'european': 133653, u'total_samples': 133653},
{u'european': 3012, u'total_samples': 3012},
{u'european': 3012, u'total_samples': 3012},
{u'european': 6616, u'total_samples': 6616},
{u'european': 6616, u'total_samples': 6616},
{u'african': 7112, u'european': 23439, u'total_samples': 30551},
{u'african': 7112, u'european': 23439, u'total_samples': 30551},
{u'african': 7112, u'european': 23439, u'total_samples': 30551},
{u'european': 2073, u'total_samples': 2073},
{u'european': 679, u'total_samples': 679},
{u'european': 679, u'total_samples': 679},
{u'european': 679, u'total_samples': 679},
{u'european': 679, u'total_samples': 679},
{u'european': 679, u'total_samples': 679},
{u'european': 679, u'total_samples': 679},
{u'european': 679, u'total_samples': 679},
{u'european': 5181, u'total_samples': 5181},
{u'european': 1657, u'total_samples': 1657},
{u'european': 1657, u'total_samples': 1657},
{u'european': 1657, u'total_samples': 1657},
{u'european': 1657, u'total_samples': 1657},
{u'european': 1657, u'total_samples': 1657},
{u'european': 1657, u'total_samples': 1657},
{u'european': 1657, u'total_samples': 1657},
{u'european': 1657, u'total_samples': 1657},
{u'european': 1657, u'total_samples': 1657},
{u'european': 1469, u'total_samples': 1469},
{u'european': 1469, u'total_samples': 1469},
{u'european': 1469, u'total_samples': 1469},
{u'european': 69395, u'total_samples': 69395},
{u'european': 69395, u'total_samples': 69395},
{u'european': 11683, u'total_samples': 11683},
{u'european': 11683, u'total_samples': 11683},
{u'european': 874, u'total_samples': 874},
{u'european': 707, u'total_samples': 707}],
u'exclusively_male_female': u'n',
u'gwas_ancestry_description': [u'European',
u'Mixed',
u'Mixed',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'Mixed',
u'Mixed',
u'Mixed',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European',
u'European'],
u'hg19': {u'chr': 6, u'pos': 26093141},
u'hupfield': u'Jan2014',
u'in_gene': u'(HFE)',
u'in_mirna_bs': u'(rs1800562(miR-564);(AF150664);(disrupts non-conserved site);GUWobble)',
u'includes_male_female_only_analyses': u'n',
u'initial_sample_description': [u'19840 EA individuals',
u'459 EA twin pairs',
u'459 EA twin pairs',
u'459 EA twin pairs',
u'459 EA twin pairs',
u'4627 European individuals',
u'4627 European individuals',
u'4627 European individuals',
u'4627 European individuals',
u'4627 European individuals',
u'4818 Australian siblings',
u'4818 Australian siblings',
u'4818 Australian siblings',
u'4818 Australian siblings',
u'4818 Australian siblings',
u'4818 Australian siblings',
u'24167 EA individuals',
u'24167 EA individuals',
u'24167 EA individuals',
u'24167 EA individuals',
u'24167 EA individuals',
u'Up to 67093 EA individuals',
u'Up to 100184 EA individuals',
u'Up to 100184 EA individuals',
u'Up to 46368 EA individuals',
u'Up to 46368 EA individuals',
u'Up to 46368 EA individuals',
u'Up to 46368 EA individuals',
u'Up to 46368 EA individuals',
u'Up to 46368 EA individuals',
u'133653 EA individuals',
u'3012 EA individuals',
u'3012 EA individuals',
u'Up to 6616 EA individuals',
u'Up to 6616 EA individuals',
[u'23439 EA', u' 7112 AA'],
[u'23439 EA', u' 7112 AA'],
[u'23439 EA', u' 7112 AA'],
[u'403 EA unrelated nonagenarians', u' 1670 controls'],
[u'336 EA cases', u' 343 EA controls'],
[u'336 EA cases', u' 343 EA controls'],
[u'336 EA cases', u' 343 EA controls'],
[u'336 EA cases', u' 343 EA controls'],
[u'336 EA cases', u' 343 EA controls'],
[u'336 EA cases', u' 343 EA controls'],
[u'336 EA cases', u' 343 EA controls'],
u'5181 Swiss individuals',
u'1657 Italian individuals',
u'1657 Italian individuals',
u'1657 Italian individuals',
u'1657 Italian individuals',
u'1657 Italian individuals',
u'1657 Italian individuals',
u'1657 Italian individuals',
u'1657 Italian individuals',
u'1657 Italian individuals',
[u'1469 unrelated European whole blood samples (473 healthy controls',
u' 453 COPD patients',
u' 383 ALS patients',
u' 111 celiac patients',
u' 49 ulcerative colitis patients)'],
[u'1469 unrelated European whole blood samples (473 healthy controls',
u' 453 COPD patients',
u' 383 ALS patients',
u' 111 celiac patients',
u' 49 ulcerative colitis patients)'],
[u'1469 unrelated European whole blood samples (473 healthy controls',
u' 453 COPD patients',
u' 383 ALS patients',
u' 111 celiac patients',
u' 49 ulcerative colitis patients)'],
u'69395 EA individuals',
u'69395 EA individuals',
u'11683 Australian individuals',
u'11683 Australian individuals',
[u'467 EA cases', u' 407 EA controls'],
u'707 EA cases'],
u'last_curation_date': u'8/17/12',
u'ls_snp': [u'(rs1800562;(1a6z',
u'1de4);(A',
u'A);(260',
u'260);(C',
u'C);(Y',
u'Y);(+',
u'+);(E',
u'E);(0',
u'0);(',
u');(0.146057',
u'0.133843);(0;0)))'],
u'platform_snps_passing_qc': [u'Affymetrix & Illumina [~2600000] (imputed)',
u'Illumina [315887]',
u'Illumina [315887]',
u'Illumina [315887]',
u'Illumina [315887]',
u'Affymetrix & Illumina [~2.11 million] (imputed)',
u'Affymetrix & Illumina [~2.11 million] (imputed)',
u'Affymetrix & Illumina [~2.11 million] (imputed)',
u'Affymetrix & Illumina [~2.11 million] (imputed)',
u'Affymetrix & Illumina [~2.11 million] (imputed)',
u'Illumina & Perlegen [427037]',
u'Illumina & Perlegen [427037]',
u'Illumina & Perlegen [427037]',
u'Illumina & Perlegen [427037]',
u'Illumina & Perlegen [427037]',
u'Illumina & Perlegen [427037]',
u'Affymetrix & Illumina [~2.5 million] (imputed)',
u'Affymetrix & Illumina [~2.5 million] (imputed)',
u'Affymetrix & Illumina [~2.5 million] (imputed)',
u'Affymetrix & Illumina [~2.5 million] (imputed)',
u'Affymetrix & Illumina [~2.5 million] (imputed)',
u'Affymetrix & Illumina [~2.5 million] (imputed)',
[u'Affymetrix', u' Illumina & Perlegen [~2.6 million] (imputed)'],
[u'Affymetrix', u' Illumina & Perlegen [~2.6 million] (imputed)'],
u'Affymetrix & Illumina [~2.5 million] (imputed)',
u'Affymetrix & Illumina [~2.5 million] (imputed)',
u'Affymetrix & Illumina [~2.5 million] (imputed)',
u'Affymetrix & Illumina [~2.5 million] (imputed)',
u'Affymetrix & Illumina [~2.5 million] (imputed)',
u'Affymetrix & Illumina [~2.5 million] (imputed)',
[u'Affymetrix', u' Illumina & Perlegen [2834208] (imputed)'],
u'Illumina [489421]',
u'Illumina [489421]',
u'Affymetrix & Illumina [~2.5 million] (imputed)',
u'Affymetrix & Illumina [~2.5 million] (imputed)',
u'Illumina [175000] (imputed)',
u'Illumina [175000] (imputed)',
u'Illumina [175000] (imputed)',
u'Illumina [516721]',
u'Illumina [331060]',
u'Illumina [331060]',
u'Illumina [331060]',
u'Illumina [331060]',
u'Illumina [331060]',
u'Illumina [331060]',
u'Illumina [331060]',
u'Affymetrix [390631] (imputed)',
u'Illumina [343866]',
u'Illumina [343866]',
u'Illumina [343866]',
u'Illumina [343866]',
u'Illumina [343866]',
u'Illumina [343866]',
u'Illumina [343866]',
u'Illumina [343866]',
u'Illumina [343866]',
u'Illumina [289044]',
u'Illumina [289044]',
u'Illumina [289044]',
[u'Affymetrix', u' Illumina & Perlegen [~2.5 million] (imputed)'],
[u'Affymetrix', u' Illumina & Perlegen [~2.5 million] (imputed)'],
[u'Illumina [610000] (imputed', u' unspecified)'],
[u'Illumina [610000] (imputed', u' unspecified)'],
u'Illumina [876476]',
u'Illumina [500000] (unspecified)'],
u'polyphen2': u'Q30201:C282Y;G>A;probablydamaging;1;0;0',
u'publication': [{u'date_pub': u'12/7/2008',
u'journal': u'Nat Genet',
u'location_within_paper': u'FullScan',
u'p_value': 0.0002503,
u'paper_phenotype_categories': u'CVD risk factor (CVD RF);Lipids',
u'paper_phenotype_description': u'Lipid level measurements',
u'phenotype': u'LDL cholesterol',
u'pmid': 19060906,
u'snpid': u'rs1800562',
u'title': u'Common variants at 30 loci contribute to polygenic dyslipidemia.'},
{u'date_pub': u'12/17/2008',
u'journal': u'Am J Hum Genet',
u'location_within_paper': u'Table 3',
u'p_value': 3.5e-11,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Ferritin levels', u' in serum'],
u'phenotype': u'Serum iron',
u'pmid': 19084217,
u'snpid': u'rs1800562',
u'title': u'Variants in TF and HFE explain approximately 40% of genetic variation in serum-transferrin levels.'},
{u'date_pub': u'12/17/2008',
u'journal': u'Am J Hum Genet',
u'location_within_paper': u'Table 3',
u'p_value': 4.3e-15,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Ferritin levels', u' in serum'],
u'phenotype': u'Transferrin saturation',
u'pmid': 19084217,
u'snpid': u'rs1800562',
u'title': u'Variants in TF and HFE explain approximately 40% of genetic variation in serum-transferrin levels.'},
{u'date_pub': u'12/17/2008',
u'journal': u'Am J Hum Genet',
u'location_within_paper': u'Table 3',
u'p_value': 4.5e-05,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Ferritin levels', u' in serum'],
u'phenotype': u'Serum ferritin',
u'pmid': 19084217,
u'snpid': u'rs1800562',
u'title': u'Variants in TF and HFE explain approximately 40% of genetic variation in serum-transferrin levels.'},
{u'date_pub': u'12/17/2008',
u'journal': u'Am J Hum Genet',
u'location_within_paper': u'Table S4',
u'p_value': 1.09e-10,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Ferritin levels', u' in serum'],
u'phenotype': u'Serum transferrin',
u'pmid': 19084217,
u'snpid': u'rs1800562',
u'title': u'Variants in TF and HFE explain approximately 40% of genetic variation in serum-transferrin levels.'},
{u'date_pub': u'10/11/2009',
u'journal': u'Nat Genet',
u'location_within_paper': u'Table 1',
u'p_value': 1.4e-23,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Platelet',
u'paper_phenotype_description': [u'Blood cell counts and traits',
u' in red and white blood cells'],
u'phenotype': u'Mean corpuscular volume (MCV)',
u'pmid': 19820697,
u'snpid': u'rs1800562',
u'title': u'A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.'},
{u'date_pub': u'10/11/2009',
u'journal': u'Nat Genet',
u'location_within_paper': u'TableS4',
u'p_value': 0.002,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Platelet',
u'paper_phenotype_description': [u'Blood cell counts and traits',
u' in red and white blood cells'],
u'phenotype': u'Mean corpuscular hemoglobin concentration (MCHC) (g/dl)',
u'pmid': 19820697,
u'snpid': u'rs1800562',
u'title': u'A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.'},
{u'date_pub': u'10/11/2009',
u'journal': u'Nat Genet',
u'location_within_paper': u'TableS4',
u'p_value': 0.00016,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Platelet',
u'paper_phenotype_description': [u'Blood cell counts and traits',
u' in red and white blood cells'],
u'phenotype': u'Hemoglobin (Hb) (g/dl)',
u'pmid': 19820697,
u'snpid': u'rs1800562',
u'title': u'A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.'},
{u'date_pub': u'10/11/2009',
u'journal': u'Nat Genet',
u'location_within_paper': u'TableS4',
u'p_value': 0.00022,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Platelet',
u'paper_phenotype_description': [u'Blood cell counts and traits',
u' in red and white blood cells'],
u'phenotype': [u'Red blood cell count (RBC) (10^12/l', u' log)'],
u'pmid': 19820697,
u'snpid': u'rs1800562',
u'title': u'A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.'},
{u'date_pub': u'10/11/2009',
u'journal': u'Nat Genet',
u'location_within_paper': u'TableS4',
u'p_value': 4.3e-22,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Platelet',
u'paper_phenotype_description': [u'Blood cell counts and traits',
u' in red and white blood cells'],
u'phenotype': u'Mean corpuscular hemoglobin (MCH) (pg)',
u'pmid': 19820697,
u'snpid': u'rs1800562',
u'title': u'A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.'},
{u'date_pub': u'10/11/2009',
u'journal': u'Nat Genet',
u'location_within_paper': u'Table 1',
u'p_value': 1.5e-08,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Hemoglobin levels', u' in serum'],
u'phenotype': u'Mean corpuscular volume (MCV)',
u'pmid': 19820699,
u'snpid': u'rs1800562',
u'title': u'Common variants in TMPRSS6 are associated with iron status and erythrocyte volume.'},
{u'date_pub': u'10/11/2009',
u'journal': u'Nat Genet',
u'location_within_paper': u'Table 1',
u'p_value': 2.2e-53,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Hemoglobin levels', u' in serum'],
u'phenotype': u'Transferrin',
u'pmid': 19820699,
u'snpid': u'rs1800562',
u'title': u'Common variants in TMPRSS6 are associated with iron status and erythrocyte volume.'},
{u'date_pub': u'10/11/2009',
u'journal': u'Nat Genet',
u'location_within_paper': u'Table 1',
u'p_value': 0.00034,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Hemoglobin levels', u' in serum'],
u'phenotype': u'Ferritin (log10)',
u'pmid': 19820699,
u'snpid': u'rs1800562',
u'title': u'Common variants in TMPRSS6 are associated with iron status and erythrocyte volume.'},
{u'date_pub': u'10/11/2009',
u'journal': u'Nat Genet',
u'location_within_paper': u'Table 1',
u'p_value': 5.1e-07,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Hemoglobin levels', u' in serum'],
u'phenotype': u'Blood hemoglobin',
u'pmid': 19820699,
u'snpid': u'rs1800562',
u'title': u'Common variants in TMPRSS6 are associated with iron status and erythrocyte volume.'},
{u'date_pub': u'10/11/2009',
u'journal': u'Nat Genet',
u'location_within_paper': u'Table 1',
u'p_value': 8.2e-19,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Hemoglobin levels', u' in serum'],
u'phenotype': u'Iron',
u'pmid': 19820699,
u'snpid': u'rs1800562',
u'title': u'Common variants in TMPRSS6 are associated with iron status and erythrocyte volume.'},
{u'date_pub': u'10/11/2009',
u'journal': u'Nat Genet',
u'location_within_paper': u'Table 1',
u'p_value': 8.5e-50,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Hemoglobin levels', u' in serum'],
u'phenotype': u'Transferrin saturation with iron',
u'pmid': 19820699,
u'snpid': u'rs1800562',
u'title': u'Common variants in TMPRSS6 are associated with iron status and erythrocyte volume.'},
{u'date_pub': u'10/11/2009',
u'journal': u'Nat Genet',
u'location_within_paper': u'Table 3',
u'p_value': 1.01e-46,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': [u'Blood cell counts and traits',
u' in red blood cells'],
u'phenotype': u'Mean corpuscular volume (MCV)',
u'pmid': 19862010,
u'snpid': u'rs1800562',
u'title': u'Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.'},
{u'date_pub': u'10/11/2009',
u'journal': u'Nat Genet',
u'location_within_paper': u'Table 3',
u'p_value': 5.74e-19,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': [u'Blood cell counts and traits',
u' in red blood cells'],
u'phenotype': u'Hemoglobin (Hb)',
u'pmid': 19862010,
u'snpid': u'rs1800562',
u'title': u'Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.'},
{u'date_pub': u'10/11/2009',
u'journal': u'Nat Genet',
u'location_within_paper': u'Table 3',
u'p_value': 7.2e-10,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': [u'Blood cell counts and traits',
u' in red blood cells'],
u'phenotype': u'Hematocrit (Hct)',
u'pmid': 19862010,
u'snpid': u'rs1800562',
u'title': u'Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.'},
{u'date_pub': u'10/11/2009',
u'journal': u'Nat Genet',
u'location_within_paper': u'Table S3',
u'p_value': 9.9e-16,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': [u'Blood cell counts and traits',
u' in red blood cells'],
u'phenotype': u'Mean corpuscular hemoglobin (MCH)',
u'pmid': 19862010,
u'snpid': u'rs1800562',
u'title': u'Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.'},
{u'date_pub': u'10/11/2009',
u'journal': u'Nat Genet',
u'location_within_paper': u'Table S5A',
u'p_value': 0.0274,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': [u'Blood cell counts and traits',
u' in red blood cells'],
u'phenotype': u'Diastolic blood pressure (DBP)',
u'pmid': 19862010,
u'snpid': u'rs1800562',
u'title': u'Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.'},
{u'date_pub': u'4/11/2010',
u'journal': u'Nat Genet',
u'location_within_paper': u'Full Scan',
u'p_value': 0.0063,
u'paper_phenotype_categories': u'Renal;Chronic kidney disease;Quantitative trait(s)',
u'paper_phenotype_description': u'Chronic kidney disease (CKD) and renal traits',
u'phenotype': u'Serum creatinine',
u'pmid': 20383146,
u'snpid': u'rs1800562',
u'title': u'New loci associated with kidney function and chronic kidney disease.'},
{u'date_pub': u'8/5/2010',
u'journal': u'Nature',
u'location_within_paper': u'Table S19',
u'p_value': 1.1e-08,
u'paper_phenotype_categories': u'CVD risk factor (CVD RF);Lipids',
u'paper_phenotype_description': u'Lipid level measurements',
u'phenotype': u'Total cholesterol',
u'pmid': 20686565,
u'snpid': u'rs1800562',
u'title': [u'Biological',
u' clinical and population relevance of 95 loci for blood lipids.']},
{u'date_pub': u'8/5/2010',
u'journal': u'Nature',
u'location_within_paper': u'Table S19',
u'p_value': 2.7e-10,
u'paper_phenotype_categories': u'CVD risk factor (CVD RF);Lipids',
u'paper_phenotype_description': u'Lipid level measurements',
u'phenotype': u'LDL cholesterol',
u'pmid': 20686565,
u'snpid': u'rs1800562',
u'title': [u'Biological',
u' clinical and population relevance of 95 loci for blood lipids.']},
{u'date_pub': u'9/21/2010',
u'journal': u'Diabetes',
u'location_within_paper': u'Table 2',
u'p_value': 2.59e-20,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': [u'Hemoglobin (HbA1c',
u' glycated hemoglobin levels)'],
u'phenotype': u'Glycated Hemoglobin (HbA1c)',
u'pmid': 20858683,
u'snpid': u'rs1800562',
u'title': u'Common variants at 10 genomic loci influence hemoglobin A\xe2??(C) levels via glycemic and nonglycemic pathways.'},
{u'date_pub': u'9/21/2010',
u'journal': u'Diabetes',
u'location_within_paper': u'Table S3',
u'p_value': 1.2e-11,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': [u'Hemoglobin (HbA1c',
u' glycated hemoglobin levels)'],
u'phenotype': u'Iron',
u'pmid': 20858683,
u'snpid': u'rs1800562',
u'title': u'Common variants at 10 genomic loci influence hemoglobin A\xe2??(C) levels via glycemic and nonglycemic pathways.'},
{u'date_pub': u'9/21/2010',
u'journal': u'Diabetes',
u'location_within_paper': u'Table S3',
u'p_value': 1.6e-12,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': [u'Hemoglobin (HbA1c',
u' glycated hemoglobin levels)'],
u'phenotype': u'Mean corpuscular volume (MCV)',
u'pmid': 20858683,
u'snpid': u'rs1800562',
u'title': u'Common variants at 10 genomic loci influence hemoglobin A\xe2??(C) levels via glycemic and nonglycemic pathways.'},
{u'date_pub': u'9/21/2010',
u'journal': u'Diabetes',
u'location_within_paper': u'Table S3',
u'p_value': 0.003,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': [u'Hemoglobin (HbA1c',
u' glycated hemoglobin levels)'],
u'phenotype': u'Hemoglobin (Hb)',
u'pmid': 20858683,
u'snpid': u'rs1800562',
u'title': u'Common variants at 10 genomic loci influence hemoglobin A\xe2??(C) levels via glycemic and nonglycemic pathways.'},
{u'date_pub': u'9/21/2010',
u'journal': u'Diabetes',
u'location_within_paper': u'Table S3',
u'p_value': 3.5e-14,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': [u'Hemoglobin (HbA1c',
u' glycated hemoglobin levels)'],
u'phenotype': u'Mean corpuscular hemoglobin (MCH)',
u'pmid': 20858683,
u'snpid': u'rs1800562',
u'title': u'Common variants at 10 genomic loci influence hemoglobin A\xe2??(C) levels via glycemic and nonglycemic pathways.'},
{u'date_pub': u'9/21/2010',
u'journal': u'Diabetes',
u'location_within_paper': u'Table S3',
u'p_value': 3.5e-15,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': [u'Hemoglobin (HbA1c',
u' glycated hemoglobin levels)'],
u'phenotype': u'Transferrin',
u'pmid': 20858683,
u'snpid': u'rs1800562',
u'title': u'Common variants at 10 genomic loci influence hemoglobin A\xe2??(C) levels via glycemic and nonglycemic pathways.'},
{u'date_pub': u'9/29/2010',
u'journal': u'Nature',
u'location_within_paper': u'Full Data',
u'p_value': 0.00947,
u'paper_phenotype_categories': u'Quantitative trait(s);Height',
u'paper_phenotype_description': u'Height',
u'phenotype': u'Height',
u'pmid': 20881960,
u'snpid': u'rs1800562',
u'title': u'Hundreds of variants clustered in genomic loci and biological pathways affect human height.'},
{u'date_pub': u'9/28/2010',
u'journal': u'PLoS One',
u'location_within_paper': u'Table 3',
u'p_value': 2.76e-09,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': [u'Blood cell counts and traits',
u' in red blood cells'],
u'phenotype': u'Mean corpuscular hemoglobin (MCH)',
u'pmid': 20927387,
u'snpid': u'rs1800562',
u'title': u'A genome-wide association study of red blood cell traits using the electronic medical record.'},
{u'date_pub': u'9/28/2010',
u'journal': u'PLoS One',
u'location_within_paper': u'Table 3',
u'p_value': 5.84e-07,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': [u'Blood cell counts and traits',
u' in red blood cells'],
u'phenotype': u'Mean corpuscular volume (MCV)',
u'pmid': 20927387,
u'snpid': u'rs1800562',
u'title': u'A genome-wide association study of red blood cell traits using the electronic medical record.'},
{u'date_pub': u'12/10/2010',
u'journal': u'Hum Mol Genet',
u'location_within_paper': u'Table S4',
u'p_value': 1.17e-09,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Ferritin and soluble transferrin receptor levels',
u' in serum'],
u'phenotype': u'Soluble transferrin receptor',
u'pmid': 21149283,
u'snpid': u'rs1800562',
u'title': u'Novel association to the proprotein convertase PCSK7 gene locus revealed by analysing soluble transferrin receptor (sTfR) levels.'},
{u'date_pub': u'12/10/2010',
u'journal': u'Hum Mol Genet',
u'location_within_paper': u'Table S5',
u'p_value': 3.02e-09,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Ferritin and soluble transferrin receptor levels',
u' in serum'],
u'phenotype': u'Serum ferritin',
u'pmid': 21149283,
u'snpid': u'rs1800562',
u'title': u'Novel association to the proprotein convertase PCSK7 gene locus revealed by analysing soluble transferrin receptor (sTfR) levels.'},
{u'date_pub': u'12/12/2010',
u'journal': u'Hum Genet',
u'location_within_paper': u'Table 3',
u'p_value': 1.4e-15,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Platelet',
u'paper_phenotype_description': [u'Blood cell counts and traits',
u' in red and white blood cells'],
u'phenotype': u'Hemoglobin (Hb)',
u'pmid': 21153663,
u'snpid': u'rs1800562',
u'title': u'Genetic association analysis highlights new loci that modulate hematological'},
{u'date_pub': u'12/12/2010',
u'journal': u'Hum Genet',
u'location_within_paper': u'Table 3',
u'p_value': 2.5e-10,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Platelet',
u'paper_phenotype_description': [u'Blood cell counts and traits',
u' in red and white blood cells'],
u'phenotype': u'Hematocrit (Hct)',
u'pmid': 21153663,
u'snpid': u'rs1800562',
u'title': u'Genetic association analysis highlights new loci that modulate hematological'},
{u'date_pub': u'12/12/2010',
u'journal': u'Hum Genet',
u'location_within_paper': u'Table 3',
u'p_value': 6.8e-16,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Platelet',
u'paper_phenotype_description': [u'Blood cell counts and traits',
u' in red and white blood cells'],
u'phenotype': u'Mean corpuscular volume (MCV)',
u'pmid': 21153663,
u'snpid': u'rs1800562',
u'title': u'Genetic association analysis highlights new loci that modulate hematological'},
{u'date_pub': u'3/12/2011',
u'journal': u'Aging Cell',
u'location_within_paper': u'Table S4',
u'p_value': 0.022,
u'paper_phenotype_categories': u'Aging;Mortality',
u'paper_phenotype_description': u'Longevity',
u'phenotype': u'Longevity',
u'pmid': 21418511,
u'snpid': u'rs1800562',
u'title': u'Genome-wide association study identifies a single major locus contributing to'},
{u'date_pub': u'3/31/2011',
u'journal': u'PLoS One',
u'location_within_paper': u'Table 2',
u'p_value': 0.00016,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': u'Iron deficiency',
u'phenotype': u'Iron deficiency (transferrin saturation)',
u'pmid': 21483845,
u'snpid': u'rs1800562',
u'title': u'Genome-wide association study identifies genetic loci associated with iron'},
{u'date_pub': u'3/31/2011',
u'journal': u'PLoS One',
u'location_within_paper': u'Table 2',
u'p_value': 1.93e-05,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': u'Iron deficiency',
u'phenotype': u'Iron deficiency (Serum iron)',
u'pmid': 21483845,
u'snpid': u'rs1800562',
u'title': u'Genome-wide association study identifies genetic loci associated with iron'},
{u'date_pub': u'3/31/2011',
u'journal': u'PLoS One',
u'location_within_paper': u'Table 2',
u'p_value': 0.022,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': u'Iron deficiency',
u'phenotype': u'Iron deficiency (Body iron)',
u'pmid': 21483845,
u'snpid': u'rs1800562',
u'title': u'Genome-wide association study identifies genetic loci associated with iron'},
{u'date_pub': u'3/31/2011',
u'journal': u'PLoS One',
u'location_within_paper': u'Table 2',
u'p_value': 2.68e-08,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': u'Iron deficiency',
u'phenotype': u'Iron deficiency (total iron-binding capacity)',
u'pmid': 21483845,
u'snpid': u'rs1800562',
u'title': u'Genome-wide association study identifies genetic loci associated with iron'},
{u'date_pub': u'3/31/2011',
u'journal': u'PLoS One',
u'location_within_paper': u'Table 2',
u'p_value': 0.039,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': u'Iron deficiency',
u'phenotype': u'Iron deficiency (serum ferritin concentration)',
u'pmid': 21483845,
u'snpid': u'rs1800562',
u'title': u'Genome-wide association study identifies genetic loci associated with iron'},
{u'date_pub': u'3/31/2011',
u'journal': u'PLoS One',
u'location_within_paper': u'Table 2',
u'p_value': 5.72e-10,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': u'Iron deficiency',
u'phenotype': u'Iron deficiency (unsaturated iron-binding capacity)',
u'pmid': 21483845,
u'snpid': u'rs1800562',
u'title': u'Genome-wide association study identifies genetic loci associated with iron'},
{u'date_pub': u'3/31/2011',
u'journal': u'PLoS One',
u'location_within_paper': u'Table 2',
u'p_value': 0.0072,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related',
u'paper_phenotype_description': u'Iron deficiency',
u'phenotype': u'Iron deficiency (serum transferrin receptor)',
u'pmid': 21483845,
u'snpid': u'rs1800562',
u'title': u'Genome-wide association study identifies genetic loci associated with iron'},
{u'date_pub': u'6/10/2011',
u'journal': u'Hum Mol Genet',
u'location_within_paper': u'Table 2',
u'p_value': 2.13e-32,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Transferrin glycosylation',
u' in serum'],
u'phenotype': u'Transferrin',
u'pmid': 21665994,
u'snpid': u'rs1800562',
u'title': u'Genome-wide association study identifies two loci strongly affecting transferrin glycosylation.'},
{u'date_pub': u'7/25/2011',
u'journal': u'J Med Genet',
u'location_within_paper': u'Table3',
u'p_value': 1.64e-10,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Hepcidin', u' in serum'],
u'phenotype': u'Ferritin (log10)',
u'pmid': 21785125,
u'snpid': u'rs1800562',
u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},
{u'date_pub': u'7/25/2011',
u'journal': u'J Med Genet',
u'location_within_paper': u'Table3',
u'p_value': 0.000636,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Hepcidin', u' in serum'],
u'phenotype': u'Log10(hepcidin/ferritin)',
u'pmid': 21785125,
u'snpid': u'rs1800562',
u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},
{u'date_pub': u'7/25/2011',
u'journal': u'J Med Genet',
u'location_within_paper': u'TableS5',
u'p_value': 0.00113,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Hepcidin', u' in serum'],
u'phenotype': u'Mean corpuscular hemoglobin concentration (MCHC)',
u'pmid': 21785125,
u'snpid': u'rs1800562',
u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},
{u'date_pub': u'7/25/2011',
u'journal': u'J Med Genet',
u'location_within_paper': u'TableS5',
u'p_value': 0.0145,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Hepcidin', u' in serum'],
u'phenotype': u'Mean corpuscular volume (MCV)',
u'pmid': 21785125,
u'snpid': u'rs1800562',
u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},
{u'date_pub': u'7/25/2011',
u'journal': u'J Med Genet',
u'location_within_paper': u'TableS5',
u'p_value': 1.7e-05,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Hepcidin', u' in serum'],
u'phenotype': u'Mean corpuscular hemoglobin (MCH)',
u'pmid': 21785125,
u'snpid': u'rs1800562',
u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},
{u'date_pub': u'7/25/2011',
u'journal': u'J Med Genet',
u'location_within_paper': u'TableS5',
u'p_value': 2.64e-15,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Hepcidin', u' in serum'],
u'phenotype': u'Transferrin saturation',
u'pmid': 21785125,
u'snpid': u'rs1800562',
u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},
{u'date_pub': u'7/25/2011',
u'journal': u'J Med Genet',
u'location_within_paper': u'TableS5',
u'p_value': 3.95e-09,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Hepcidin', u' in serum'],
u'phenotype': u'Iron',
u'pmid': 21785125,
u'snpid': u'rs1800562',
u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},
{u'date_pub': u'7/25/2011',
u'journal': u'J Med Genet',
u'location_within_paper': u'TableS5',
u'p_value': 0.0428,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Hepcidin', u' in serum'],
u'phenotype': u'Hemoglobin (Hb)',
u'pmid': 21785125,
u'snpid': u'rs1800562',
u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},
{u'date_pub': u'7/25/2011',
u'journal': u'J Med Genet',
u'location_within_paper': u'TableS5',
u'p_value': 4.95e-11,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Hepcidin', u' in serum'],
u'phenotype': u'Transferrin',
u'pmid': 21785125,
u'snpid': u'rs1800562',
u'title': u'Association of HFE and TMPRSS6 genetic variants with iron and erythrocyte parameters is only in part dependent on serum hepcidin concentrations.'},
{u'date_pub': u'8/4/2011',
u'journal': u'PLoS Genet',
u'location_within_paper': u'TableS7',
u'p_value': 2.9e-07,
u'paper_phenotype_categories': u'Quantitative trait(s);Gene expression (RNA);Blood-related',
u'paper_phenotype_description': u'Gene expression in blood cells',
u'phenotype': u'Gene expression of ALAS2 in blood',
u'pmid': 21829388,
u'snpid': u'rs1800562',
u'title': u'Trans-eQTLs Reveal That Independent Genetic Variants Associated with a Complex'},
{u'date_pub': u'8/4/2011',
u'journal': u'PLoS Genet',
u'location_within_paper': u'TableS7',
u'p_value': 4.4e-06,
u'paper_phenotype_categories': u'Quantitative trait(s);Gene expression (RNA);Blood-related',
u'paper_phenotype_description': u'Gene expression in blood cells',
u'phenotype': u'Gene expression of [probe 2940446 centered at chr20:36199875] in blood',
u'pmid': 21829388,
u'snpid': u'rs1800562',
u'title': u'Trans-eQTLs Reveal That Independent Genetic Variants Associated with a Complex'},
{u'date_pub': u'8/4/2011',
u'journal': u'PLoS Genet',
u'location_within_paper': u'TableS7',
u'p_value': 8.6e-06,
u'paper_phenotype_categories': u'Quantitative trait(s);Gene expression (RNA);Blood-related',
u'paper_phenotype_description': u'Gene expression in blood cells',
u'phenotype': u'Gene expression of ADHFE1 in blood',
u'pmid': 21829388,
u'snpid': u'rs1800562',
u'title': u'Trans-eQTLs Reveal That Independent Genetic Variants Associated with a Complex'},
{u'date_pub': u'9/11/2011',
u'journal': u'Nature',
u'location_within_paper': u'TableS4',
u'p_value': 0.01592528,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood pressure;CVD risk factor (CVD RF)',
u'paper_phenotype_description': u'Blood pressure',
u'phenotype': u'Systolic blood pressure (SBP)',
u'pmid': 21909115,
u'snpid': u'rs1800562',
u'title': u'Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk.'},
{u'date_pub': u'9/11/2011',
u'journal': u'Nature',
u'location_within_paper': u'TableS4',
u'p_value': 7.26329e-07,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood pressure;CVD risk factor (CVD RF)',
u'paper_phenotype_description': u'Blood pressure',
u'phenotype': u'Diastolic blood pressure (DBP)',
u'pmid': 21909115,
u'snpid': u'rs1800562',
u'title': u'Genetic variants in novel pathways influence blood pressure and cardiovascular disease risk.'},
{u'date_pub': u'9/24/2011',
u'journal': u'BMC Med Genet',
u'location_within_paper': u'Table S4',
u'p_value': 4.7e-12,
u'paper_phenotype_categories': u'Quantitative trait(s);CVD risk factor (CVD RF);Lipids;Weight;Body mass index;Hepatic;Blood-related;C-reactive protein (CRP)',
u'paper_phenotype_description': [u'Biomarkers (liver function',
u' butrylycholinesterase',
u' CRP',
u' ferritin',
u' glucose',
u' HDL cholesterol',
u' insulin',
u' LDL cholesterol',
u' triglycerides',
u' uric acid)',
u' body mass index (BMI)'],
u'phenotype': u'Ferritin',
u'pmid': 21943158,
u'snpid': u'rs1800562',
u'title': [u'Genetic variants in LPL',
u' OASL and TOMM40/APOE-C1-C2-C4 genes are associated with multiple cardiovascular-related traits.']},
{u'date_pub': u'9/24/2011',
u'journal': u'BMC Med Genet',
u'location_within_paper': u'Table S4',
u'p_value': 0.008,
u'paper_phenotype_categories': u'Quantitative trait(s);CVD risk factor (CVD RF);Lipids;Weight;Body mass index;Hepatic;Blood-related;C-reactive protein (CRP)',
u'paper_phenotype_description': [u'Biomarkers (liver function',
u' butrylycholinesterase',
u' CRP',
u' ferritin',
u' glucose',
u' HDL cholesterol',
u' insulin',
u' LDL cholesterol',
u' triglycerides',
u' uric acid)',
u' body mass index (BMI)'],
u'phenotype': u'LDL cholesterol',
u'pmid': 21943158,
u'snpid': u'rs1800562',
u'title': [u'Genetic variants in LPL',
u' OASL and TOMM40/APOE-C1-C2-C4 genes are associated with multiple cardiovascular-related traits.']},
{u'date_pub': u'11/5/2011',
u'journal': u'Psychiatr Genet',
u'location_within_paper': u'TableS1',
u'p_value': 0.02562,
u'paper_phenotype_categories': u'Neuro;Behavioral;Depression;Alcohol;Addiction',
u'paper_phenotype_description': u'Comorbid depressive syndrome and alcohol dependence',
u'phenotype': u'Comorbid depressive syndrome and alcohol dependence',
u'pmid': 22064162,
u'snpid': u'rs1800562',
u'title': u'Genome-wide association study of comorbid depressive syndrome and alcohol dependence.'},
{u'date_pub': u'11/16/2011',
u'journal': u'Hepatology',
u'location_within_paper': u'Table 6',
u'p_value': 0.033,
u'paper_phenotype_categories': u'Quantitative trait(s);Blood-related;Serum',
u'paper_phenotype_description': [u'Ferritin levels', u' in serum'],
u'phenotype': u'Serum ferritin levels in HCV-infected individuals',
u'pmid': 22095909,
u'snpid': u'rs1800562',
u'title': u'Serum ferritin levels are associated with a distinct phenotype of chronic hepatitis C poorly responding to pegylated interferon-alpha and ribavirin therapy.'}],
u'replication': [{u'european': 20623, u'total_samples': 20623},
{u'european': 9316, u'total_samples': 9316},
{u'european': 9316, u'total_samples': 9316},
{u'european': 9316, u'total_samples': 9316},
{u'european': 9316, u'total_samples': 9316},
{u'european': 9316, u'total_samples': 9316},
{u'european': 3470, u'total_samples': 3470},
{u'european': 3470, u'total_samples': 3470},
{u'european': 3470, u'total_samples': 3470},
{u'european': 3470, u'total_samples': 3470},
{u'european': 3470, u'total_samples': 3470},
{u'european': 3470, u'total_samples': 3470},
{u'european': 9456, u'total_samples': 9456},
{u'european': 9456, u'total_samples': 9456},
{u'european': 9456, u'total_samples': 9456},
{u'european': 9456, u'total_samples': 9456},
{u'european': 9456, u'total_samples': 9456},
{u'european': 22982, u'total_samples': 22982},
{u'african': 8061,
u'east_asian': 15046,
u'european': 7063,
u'indian_south_asian': 9705,
u'total_samples': 39875},
{u'african': 8061,
u'east_asian': 15046,
u'european': 7063,
u'indian_south_asian': 9705,
u'total_samples': 39875},
{u'european': 50074, u'total_samples': 50074},
{u'european': 11731, u'total_samples': 11731},
{u'european': 232, u'total_samples': 232},
{u'european': 232, u'total_samples': 232},
{u'european': 232, u'total_samples': 232},
{u'european': 232, u'total_samples': 232},
{u'european': 232, u'total_samples': 232},
{u'european': 232, u'total_samples': 232},
{u'european': 232, u'total_samples': 232},
{u'european': 2284, u'total_samples': 2284},
{u'european': 1786, u'total_samples': 1786},
{u'european': 1786, u'total_samples': 1786},
{u'european': 1786, u'total_samples': 1786},
{u'european': 133661, u'total_samples': 133661},
{u'european': 133661, u'total_samples': 133661}],
u'replication_sample_description': [u'Up to 20623 EA individuals',
u'NR',
u'NR',
u'NR',
u'NR',
u'9316 European individuals',
u'9316 European individuals',
u'9316 European individuals',
u'9316 European individuals',
u'9316 European individuals',
u'3470 Dutch individuals',
u'3470 Dutch individuals',
u'3470 Dutch individuals',
u'3470 Dutch individuals',
u'3470 Dutch individuals',
u'3470 Dutch individuals',
u'9456 EA individuals',
u'9456 EA individuals',
u'9456 EA individuals',
u'9456 EA individuals',
u'9456 EA individuals',
u'Up to 22982 EA individuals',
[u'9705 South Asians',
u' 15046 East Asians',
u' 8061 African Americans',
u' 7063 Europeans'],
[u'9705 South Asians',
u' 15046 East Asians',
u' 8061 African Americans',
u' 7063 Europeans'],
u'NR',
u'NR',
u'NR',
u'NR',
u'NR',
u'NR',
u'50074 EA individuals',
u'NR',
u'NR',
u'NR',
u'NR',
u'NR',
u'NR',
u'NR',
[u'4149 EA (specified or presumed) nonagenarian cases', u' 7582 controls'],
u'71 EA cases and 161 EA controls',
u'71 EA cases and 161 EA controls',
u'71 EA cases and 161 EA controls',
u'71 EA cases and 161 EA controls',
u'71 EA cases and 161 EA controls',
u'71 EA cases and 161 EA controls',
u'71 EA cases and 161 EA controls',
u'2284 Australian individuals',
u'NR',
u'NR',
u'NR',
u'NR',
u'NR',
u'NR',
u'NR',
u'NR',
u'NR',
[u'1490 European ancestry blood samples',
u' 74 Dutch liver samples',
u' 62 Dutch muscle samples',
u' 83 Dutch subcutaneous adipose samples',
u' 77 visceral adipose samples'],
[u'1490 European ancestry blood samples',
u' 74 Dutch liver samples',
u' 62 Dutch muscle samples',
u' 83 Dutch subcutaneous adipose samples',
u' 77 visceral adipose samples'],
[u'1490 European ancestry blood samples',
u' 74 Dutch liver samples',
u' 62 Dutch muscle samples',
u' 83 Dutch subcutaneous adipose samples',
u' 77 visceral adipose samples'],
u'133661 EA individuals',
u'133661 EA individuals',
u'NR',
u'NR',
u'NR',
u'NR'],
u'sift': u'C282Y:(C>Y);(1.00>0.00);(TOLERATED>DELETERIOUS)',
u'srsid': 1800562,
u'uniprot': u'(HFE;TOPO_DOM;23-306;Extracellular (Potential).);(HFE;DOMAIN;207-298;Ig-like C1-type.);(HFE;REGION;206-297;Alpha-3.);(HFE;DISULFID;225-282;26200948);(HFE;VARIANT;282-282;C -> Y (in HH; the frequency of the Tyr- 282 mutation is higher in patients with type 2 diabetes than it is in the general population of healthy subjects; dbSNP:rs1800562). /FTId=VAR_004398.);(HFE;STRAND;280-285;26201113)'},
u'gwassnps': {u'genename': u'HFE',
u'pubmed': 24097068,
u'pvalue': u'8E-14',
u'pvalue_desc': u'',
u'region': u'6p22.2',
u'risk_allele': u'rs1800562-A',
u'risk_allele_freq': u'0.07',
u'rsid': u'rs1800562',
u'title': u'Discovery and refinement of loci associated with lipid levels.',
u'trait': u'LDL cholesterol'},
u'mutdb': {u'alt': u'A',
u'chrom': u'6',
u'hg19': {u'end': 26093141, u'start': 26093141},
u'mutpred_score': 0.773,
u'ref': u'G',
u'rsid': u'rs1800562',
u'strand': u'p',
u'uniprot_id': u'VAR_004398'},
u'query': u'RCV000000019',
u'wellderly': {u'adviser_score': u'6~Haemochromatosis, association with~Common, Known Causative Mutation',
u'allele_aa': u'Y',
u'alleles': [{u'allele': u'A', u'freq': 0.04},
{u'allele': u'G', u'freq': 0.96}],
u'alt': u'A',
u'chrom': u'6',
u'coding_impact': u'Nonsynonymous',
u'gene': u'HFE',
u'genotypes': [{u'count': 16, u'freq': 0.08, u'genotype': u'G/A'},
{u'count': 184, u'freq': 0.92, u'genotype': u'G/G'}],
u'hg19': {u'end': 26093141, u'start': 26093141},
u'original_aa': u'C',
u'pos': 26093141,
u'protein_pos': [u'259',
u'279',
u'194',
u'282',
u'180',
u'268',
u'176',
u'190',
u'102'],
u'ref': u'G',
u'sift': u'INTOLERANT',
u'vartype': u'snp'}},
{u'_id': u'chr14:g.77902228G>A',
u'_score': 16.533625,
u'cadd': {u'_license': u'http://goo.gl/bkpNhq',
u'alt': u'A',
u'anc': u'G',
u'annotype': u'CodingTranscript',
u'bstatistic': 626,
u'chmm': {u'bivflnk': 0.0,
u'enh': 0.008,
u'enhbiv': 0.0,
u'het': 0.0,
u'quies': 0.016,
u'reprpc': 0.0,
u'reprpcwk': 0.0,
u'tssa': 0.0,
u'tssaflnk': 0.0,
u'tssbiv': 0.0,
u'tx': 0.748,
u'txflnk': 0.0,
u'txwk': 0.228,
u'znfrpts': 0.0},
u'chrom': 14,
u'consdetail': u'stop_gained',
u'consequence': u'STOP_GAINED',
u'consscore': 8,
u'cpg': 0.04,
u'dna': {u'helt': -2.68, u'mgw': 0.17, u'prot': 1.79, u'roll': -1.14},
u'encode': {u'exp': 95.92,
u'h3k27ac': 10.28,
u'h3k4me1': 4.32,
u'h3k4me3': 4.0,
u'nucleo': 1.2},
u'exon': u'13/20',
u'fitcons': 0.701516,
u'gc': 0.42,
u'gene': {u'ccds_id': u'CCDS9862.1',
u'cds': {u'cdna_pos': 1382,
u'cds_pos': 871,
u'rel_cdna_pos': 0.47,
u'rel_cds_pos': 0.59},
u'feature_id': u'ENST00000553888',
u'gene_id': u'ENSG00000151445',
u'genename': u'VIPAS39',
u'prot': {u'domain': u'ndomain', u'protpos': 291, u'rel_prot_pos': 0.59}},
u'gerp': {u'n': 5.17, u'rs': 359.5, u'rs_pval': 1.2817e-55, u's': 4.26},
u'isderived': u'TRUE',
u'isknownvariant': u'FALSE',
u'istv': u'FALSE',
u'length': 0,
u'mapability': {u'20bp': 1, u'35bp': 1},
u'min_dist_tse': 714,
u'min_dist_tss': 7277,
u'mutindex': 46,
u'naa': u'*',
u'oaa': u'Q',
u'phast_cons': {u'mammalian': 0.966,
u'primate': 0.986,
u'vertebrate': 0.999},
u'phred': 39,
u'phylop': {u'mammalian': 1.275, u'primate': 0.645, u'vertebrate': 3.95},
u'pos': 77902228,
u'rawscore': 12.441084,
u'ref': u'G',
u'segway': u'R1',
u'type': u'SNV'},
u'clinvar': {u'allele_id': 15153,
u'alt': u'A',
u'chrom': u'14',
u'cytogenic': u'14q24.3',
u'gene': {u'id': u'63894', u'symbol': u'VIPAS39'},
u'hg19': {u'end': 77902228, u'start': 77902228},
u'hg38': {u'end': 77435885, u'start': 77435885},
u'hgvs': {u'coding': [u'NM_001193315.1:c.871C>T', u'NM_022067.3:c.871C>T'],
u'genomic': [u'NG_023421.1:g.26756C>T',
u'NC_000014.9:g.77435885G>A',
u'NC_000014.8:g.77902228G>A']},
u'omim': u'613401.0004',
u'rcv': {u'accession': u'RCV000000134',
u'clinical_significance': u'Pathogenic',
u'conditions': {u'age_of_onset': u'Neonatal',
u'identifiers': {u'medgen': u'C3150672',
u'omim': u'613404',
u'orphanet': u'2697'},
u'name': u'Arthrogryposis, renal dysfunction, and cholestasis 2 (ARCS2)'},
u'last_evaluated': u'2010-04-01',
u'number_submitters': 1,
u'origin': u'germline',
u'preferred_name': u'NM_022067.3(VIPAS39):c.871C>T (p.Gln291Ter)',
u'review_status': u'no assertion criteria provided'},
u'ref': u'G',
u'rsid': u'rs267607171',
u'type': u'single nucleotide variant',
u'variant_id': 114},
u'dbnsfp': {u'aa': {u'alt': u'X',
u'codonpos': 1,
u'pos': [u'291', u'291', u'242', u'291', u'242', u'317'],
u'ref': u'Q',
u'refcodon': u'CAG'},
u'alt': u'A',
u'ancestral_allele': u'G',
u'cds_strand': u'-',
u'chrom': u'14',
u'clinvar': {u'clinsig': 5,
u'rs': u'rs267607171',
u'trait': u'Arthrogryposis\\x2c_renal_dysfunction\\x2c_and_cholestasis_2'},
u'ensembl': {u'geneid': u'ENSG00000151445',
u'proteinid': [u'ENSP00000339122',
u'ENSP00000452181',
u'ENSP00000313098',
u'ENSP00000452191',
u'ENSP00000404815',
u'ENSP00000451857'],
u'transcriptid': [u'ENST00000343765',
u'ENST00000553888',
u'ENST00000327028',
u'ENST00000557658',
u'ENST00000448935',
u'ENST00000556412']},
u'fathmm-mkl': {u'coding_group': u'AEFGBI',
u'coding_pred': u'D',
u'coding_rankscore': 0.7169,
u'coding_score': 0.96959},
u'genename': u'VIPAS39',
u'gerp++': {u'nr': 5.17, u'rs': 4.26, u'rs_rankscore': 0.49573},
u'gm12878': {u'confidence_value': 0,
u'fitcons_rankscore': 0.89268,
u'fitcons_score': 0.724815},
u'h1-hesc': {u'confidence_value': 0,
u'fitcons_rankscore': 0.93697,
u'fitcons_score': 0.732669},
u'hg18': {u'end': 76971981, u'start': 76971981},
u'hg19': {u'end': 77902228, u'start': 77902228},
u'hg38': {u'end': 77435885, u'start': 77435885},
u'huvec': {u'confidence_value': 0,
u'fitcons_rankscore': 0.83205,
u'fitcons_score': 0.714379},
u'integrated': {u'confidence_value': 0,
u'fitcons_rankscore': 0.97429,
u'fitcons_score': 0.736574},
u'lrt': {u'converted_rankscore': 0.62918,
u'omega': 0.150383,
u'pred': u'D',
u'score': 9e-06},
u'mutationtaster': {u'AAE': [u'Q278*',
u'Q317*',
u'Q242*',
u'Q291*',
u'Q291*',
u'Q291*'],
u'converted_rankscore': 0.81033,
u'model': [u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae',
u'complex_aae'],
u'pred': [u'A', u'A', u'A', u'A', u'A', u'A'],
u'score': [1, 1, 1, 1, 1, 1]},
u'phastcons': {u'20way': {u'mammalian': 0.998,
u'mammalian_rankscore': 0.69624},
u'7way': {u'vertebrate': 0.972, u'vertebrate_rankscore': 0.45462}},
u'phylo': {u'p20way': {u'mammalian': 1.048,
u'mammalian_rankscore': 0.71188},
u'p7way': {u'vertebrate': 0.83, u'vertebrate_rankscore': 0.35896}},
u'ref': u'G',
u'rsid': u'rs267607171',
u'siphy_29way': {u'logodds': 14.8639,
u'logodds_rankscore': 0.69849,
u'pi': {u'a': 0.0, u'c': 0.0, u'g': 0.855, u't': 0.145}}},
u'dbsnp': {u'allele_origin': u'unspecified',
u'alleles': [{u'allele': u'G'}, {u'allele': u'A'}],
u'alt': u'A',
u'chrom': u'14',
u'class': u'SNV',
u'dbsnp_build': 137,
u'flags': [u'ASP', u'LSD', u'NSN', u'PM', u'REF', u'RV'],
u'gene': {u'geneid': u'63894', u'symbol': u'VIPAS39'},
u'hg19': {u'end': 77902229, u'start': 77902228},
u'ref': u'G',
u'rsid': u'rs267607171',
u'validated': False,
u'var_subtype': u'ts',
u'vartype': u'snp'},
u'query': u'RCV000000134',
u'snpeff': {u'ann': [{u'cdna': {u'length': u'2969', u'position': u'1417'},
u'cds': {u'length': u'1482', u'position': u'871'},
u'effect': u'stop_gained',
u'feature_id': u'NM_001193314.1',
u'feature_type': u'transcript',
u'gene_id': u'VIPAS39',
u'gene_name': u'VIPAS39',
u'hgvs_c': u'c.871C>T',
u'hgvs_p': u'p.Gln291*',
u'protein': {u'length': u'493', u'position': u'291'},
u'putative_impact': u'HIGH',
u'rank': u'13',
u'total': u'20',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2569', u'position': u'1017'},
u'cds': {u'length': u'1482', u'position': u'871'},
u'effect': u'stop_gained',
u'feature_id': u'NM_001193315.1',
u'feature_type': u'transcript',
u'gene_id': u'VIPAS39',
u'gene_name': u'VIPAS39',
u'hgvs_c': u'c.871C>T',
u'hgvs_p': u'p.Gln291*',
u'protein': {u'length': u'493', u'position': u'291'},
u'putative_impact': u'HIGH',
u'rank': u'13',
u'total': u'20',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2422', u'position': u'870'},
u'cds': {u'length': u'1335', u'position': u'724'},
u'effect': u'stop_gained',
u'feature_id': u'NM_001193316.1',
u'feature_type': u'transcript',
u'gene_id': u'VIPAS39',
u'gene_name': u'VIPAS39',
u'hgvs_c': u'c.724C>T',
u'hgvs_p': u'p.Gln242*',
u'protein': {u'length': u'444', u'position': u'242'},
u'putative_impact': u'HIGH',
u'rank': u'12',
u'total': u'19',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2746', u'position': u'1194'},
u'cds': {u'length': u'1482', u'position': u'871'},
u'effect': u'stop_gained',
u'feature_id': u'NM_001193317.1',
u'feature_type': u'transcript',
u'gene_id': u'VIPAS39',
u'gene_name': u'VIPAS39',
u'hgvs_c': u'c.871C>T',
u'hgvs_p': u'p.Gln291*',
u'protein': {u'length': u'493', u'position': u'291'},
u'putative_impact': u'HIGH',
u'rank': u'13',
u'total': u'20',
u'transcript_biotype': u'Coding'},
{u'cdna': {u'length': u'2840', u'position': u'1288'},
u'cds': {u'length': u'1482', u'position': u'871'},
u'effect': u'stop_gained',
u'feature_id': u'NM_022067.3',
u'feature_type': u'transcript',
u'gene_id': u'VIPAS39',
u'gene_name': u'VIPAS39',
u'hgvs_c': u'c.871C>T',
u'hgvs_p': u'p.Gln291*',
u'protein': {u'length': u'493', u'position': u'291'},
u'putative_impact': u'HIGH',
u'rank': u'14',
u'total': u'21',
u'transcript_biotype': u'Coding'}],
u'lof': {u'gene_id': u'VIPAS39',
u'gene_name': u'VIPAS39',
u'number_of_transcripts_in_gene': u'5',
u'percent_of_transcripts_affected': u'1.00'},
u'nmd': {u'gene_id': u'VIPAS39',
u'gene_name': u'VIPAS39',
u'number_of_transcripts_in_gene': u'5',
u'percent_of_transcripts_affected': u'1.00'}},
u'vcf': {u'alt': u'A', u'position': u'77902228', u'ref': u'G'}}]
Yes, you can. If you pass an id list (i.e., xli above) larger than 1000 ids, we will do the id mapping in-batch with 1000 ids at a time, and then concatenate the results all together for you. So, from the user-end, it's exactly the same as passing a shorter list. You don't need to worry about saturating our backend servers.