ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.1820A>C (p.Lys607Thr) (rs55962656)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163031 SCV000213519 likely benign Hereditary cancer-predisposing syndrome 2016-09-29 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Other data supporting benign classification,In silico models in agreement (benign)
Breast Cancer Information Core (BIC) (BRCA2) RCV000077269 SCV000145958 uncertain significance Breast-ovarian cancer, familial 2 2002-06-20 no assertion criteria provided clinical testing
Color RCV000163031 SCV000911866 likely benign Hereditary cancer-predisposing syndrome 2018-01-08 criteria provided, single submitter clinical testing
Counsyl RCV000077269 SCV000785309 likely benign Breast-ovarian cancer, familial 2 2017-07-05 criteria provided, single submitter clinical testing
GeneDx RCV000436051 SCV000512343 likely benign not specified 2016-05-05 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Integrated Genetics/Laboratory Corporation of America RCV000436051 SCV000694572 likely benign not specified 2018-02-05 criteria provided, single submitter clinical testing Variant summary: BRCA2 c.1820A>C (p.Lys607Thr) results in a non-conservative amino acid change in the encoded protein sequence. Three of four in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 3e-05 in 236036 control chromosomes in gnomAD and literature. This frequency is not significantly higher than expected for a pathogenic variant in BRCA2 causing Hereditary Breast and Ovarian Cancer (3e-05 vs 7.50E-04), allowing no conclusion about variant significance. c.1820A>C has been reported in the literature in individuals affected with Hereditary Breast and Ovarian Cancer (Spurdle_2008) without strong evidence for pathogenicity. Co-occurrences with other pathogenic variant(s) have been reported (BRCA1 c.5563_5563delinsGGATCC, p.Ile1856insGly; BRCA1 c.5503C>T, p.Arg1835X; BRCA2 c.7558C>T, p.Arg2520X), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as likely benign.
Invitae RCV000043901 SCV000071914 likely benign Hereditary breast and ovarian cancer syndrome 2017-09-05 criteria provided, single submitter clinical testing
Mendelics RCV000043901 SCV000838764 uncertain significance Hereditary breast and ovarian cancer syndrome 2018-07-02 criteria provided, single submitter clinical testing
Sharing Clinical Reports Project (SCRP) RCV000077269 SCV000109066 benign Breast-ovarian cancer, familial 2 2012-05-01 no assertion criteria provided clinical testing

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