ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.5882G>A (p.Ser1961Asn) (rs80358820)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000044784 SCV000072797 likely benign not provided 2019-03-02 criteria provided, single submitter clinical testing
Ambry Genetics RCV000128953 SCV000172831 likely benign Hereditary cancer-predisposing syndrome 2018-11-21 criteria provided, single submitter clinical testing In silico models in agreement (benign);Other strong data supporting benign classification
GeneDx RCV000439783 SCV000512372 likely benign not specified 2018-01-10 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 RCV000439783 SCV000694914 uncertain significance not specified 2019-01-21 criteria provided, single submitter clinical testing Variant summary: BRCA2 c.5882G>A (p.Ser1961Asn) results in a conservative amino acid change located in the BRCA2 repeat region, between the repeats BRC6 and BRC7 (IPR002093) of the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 8.1e-06 in 246088 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.5882G>A has been reported in the literature in individuals affected with Hereditary Breast and Ovarian Cancer (Blay_2013, Infante_2006, Velasco_2005). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Breast and Ovarian Cancer. Co-occurrences with other pathogenic variant(s) have been reported (BRCA1 c.3331_3334delCAAG, p.Gln1111fsX5 in the BIC database), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four other ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant, three times as likely benign and once as uncertain significance. Based on the evidence outlined above, the variant was classified as VUS-possibly benign.
Counsyl RCV000031585 SCV000784831 uncertain significance Breast-ovarian cancer, familial 2 2017-01-04 criteria provided, single submitter clinical testing
Color RCV000128953 SCV000903520 benign Hereditary cancer-predisposing syndrome 2016-12-21 criteria provided, single submitter clinical testing
Mendelics RCV000031585 SCV001139129 likely benign Breast-ovarian cancer, familial 2 2019-05-28 criteria provided, single submitter clinical testing
Sharing Clinical Reports Project (SCRP) RCV000031585 SCV000054191 benign Breast-ovarian cancer, familial 2 2012-03-12 no assertion criteria provided clinical testing
Breast Cancer Information Core (BIC) (BRCA2) RCV000031585 SCV000146722 uncertain significance Breast-ovarian cancer, familial 2 2002-06-20 no assertion criteria provided clinical testing

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