ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.5710C>G (p.Leu1904Val) (rs55875643)

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Total submissions: 16
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) RCV000031571 SCV000244459 benign Breast-ovarian cancer, familial 2 2015-08-10 reviewed by expert panel curation IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 1 based on posterior probability = 0.0000209
Invitae RCV000433189 SCV000072737 benign not provided 2019-02-20 criteria provided, single submitter clinical testing
CSER _CC_NCGL, University of Washington RCV000148433 SCV000190132 likely benign Neoplasm of the breast 2014-06-01 criteria provided, single submitter research
GeneDx RCV000044724 SCV000210618 likely benign not specified 2018-02-27 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.
Ambry Genetics RCV000162807 SCV000213288 benign Hereditary cancer-predisposing syndrome 2014-11-19 criteria provided, single submitter clinical testing
Counsyl RCV000031571 SCV000488170 benign Breast-ovarian cancer, familial 2 2016-01-13 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000433189 SCV000511375 likely benign not provided 2017-02-08 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000044724 SCV000591990 uncertain significance not specified 2013-11-13 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000044724 SCV000593747 likely benign not specified 2016-10-07 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000044724 SCV000600659 likely benign not specified 2017-05-24 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000433189 SCV000694893 benign not provided 2016-08-22 criteria provided, single submitter clinical testing Variant summary: The BRCA2 c.5710C>G (p.Leu1904Val) variant causes a missense change involving a non-conserved nucleotide with 4/4 in silico tools (SNPs&GO not captured due to low reliability index) predict a benign outcome, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 5/120788 (1/24160), which does not exceed the estimated maximal expected allele frequency for a pathogenic BRCA2 variant of 1/1333. Multiple publications and databases cite the variant in affected individuals, in which multiple individuals carried another pathogenic BRCA2 variant (c.3922G>T (p.Glu1308X), c.1813dup (p.Ile605AsnfsX11)) and BRCA1 (c.5324T>G (p.Met1775Arg - classified as pathogenic by LCA) and c.1949_1950delTA (p.Ile650LysfsX22)). In addition, multiple reputable clinical laboratories classify the variant as "likely benign/benign." Therefore, the variant of interest has been classified as Benign.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000433189 SCV000889076 benign not provided 2018-09-06 criteria provided, single submitter clinical testing
Color RCV000162807 SCV000902851 benign Hereditary cancer-predisposing syndrome 2016-04-21 criteria provided, single submitter clinical testing
Mendelics RCV000031571 SCV001139123 likely benign Breast-ovarian cancer, familial 2 2019-05-28 criteria provided, single submitter clinical testing
Sharing Clinical Reports Project (SCRP) RCV000031571 SCV000054176 benign Breast-ovarian cancer, familial 2 2012-12-05 no assertion criteria provided clinical testing
Breast Cancer Information Core (BIC) (BRCA2) RCV000031571 SCV000146671 uncertain significance Breast-ovarian cancer, familial 2 2002-05-29 no assertion criteria provided clinical testing

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