ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.4656T>C (p.Gly1552=) (rs41293491)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000131764 SCV000186808 likely benign Hereditary cancer-predisposing syndrome 2014-08-11 criteria provided, single submitter clinical testing
Breast Cancer Information Core (BIC) (BRCA2) RCV000113328 SCV000146463 benign Breast-ovarian cancer, familial 2 2002-05-29 no assertion criteria provided clinical testing
Color RCV000131764 SCV000683641 likely benign Hereditary cancer-predisposing syndrome 2015-07-15 criteria provided, single submitter clinical testing
Counsyl RCV000113328 SCV000220860 likely benign Breast-ovarian cancer, familial 2 2014-11-07 criteria provided, single submitter literature only
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000123975 SCV000591917 benign not specified 2012-04-18 criteria provided, single submitter clinical testing
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) RCV000113328 SCV000578870 likely benign Breast-ovarian cancer, familial 2 2017-06-29 reviewed by expert panel curation Synonymous substitution variant, with low bioinformatic likelihood to result in a splicing aberration (Splicing prior probability 0.02; http://priors.hci.utah.edu/PRIORS/).
GeneDx RCV000123975 SCV000167368 benign not specified 2014-05-20 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 RCV000589392 SCV000694792 likely benign not provided 2016-04-18 criteria provided, single submitter clinical testing Variant summary: The variant of interest involves the alteration of a non-conserved nucleotide and results in a synonymous change. Mutation taster predicts neutral outcome for this change and in silico tools via Alamut predict no significant impact on splicing. The variant was observed exclusively in the Non-Finnish European subcohort of the ExAC project at an allele frequency of 0.009% which does not exceed the maximal expected allele frequency of a disease causing BRCA2 variant (0.075%). To our knowledge, the variant was not reported in HBOC spectrum patients and in vivo/vitro studies to describe the functional impact of the variant were not reported in the literature at the time of scoring. Clinical diagnostic laboratories classify variant as Benign/Likely Benign via ClinVar without evidence to independently evaluate. A co-occurrence of the variant of interest with a potentially pathogenic BRCA1 variant (c.5161C>T (p.Gln1721X) was reported by UMD indicating neutrality. Considering all evidence, the variant was classified as likely benign.
Invitae RCV000044463 SCV000072476 benign Hereditary breast and ovarian cancer syndrome 2017-12-26 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000123975 SCV000538479 likely benign not specified 2016-12-02 criteria provided, single submitter clinical testing Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: This variant has not been reported in affected individuals. It is present in HGMD (classified as DM) in a publication describing a method for detecting variants. This variant is classified in ClinVar with 1 star as Benign or Likely Benign by 5 submitters: BIC, Invitae, Ambry, GeneDx, Counsyl. It is present in ExAC with a Max MAF of 0.009% (6 European alleles) and in gnomAD with a MaxMAF of 0.01% (14 European alleles).
PreventionGenetics RCV000589392 SCV000805711 likely benign not provided 2017-02-23 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000589392 SCV000889058 likely benign not provided 2018-08-07 criteria provided, single submitter clinical testing

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