ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.9085G>A (p.Ala3029Thr) (rs56179254)

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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001083149 SCV000073720 benign Hereditary breast and ovarian cancer syndrome 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000129046 SCV000172960 benign Hereditary cancer-predisposing syndrome 2014-08-07 criteria provided, single submitter clinical testing
GeneDx RCV000045707 SCV000210494 likely benign not specified 2018-01-22 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.
A.C.Camargo Cancer Center / LGBM, A.C.Camargo Cancer Center RCV000413118 SCV000492499 uncertain significance Neoplasm of the breast criteria provided, single submitter research
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000045707 SCV000592253 likely benign not specified 2017-02-07 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000045707 SCV000600840 likely benign not specified 2017-04-20 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587355 SCV000695203 benign not provided 2017-07-27 criteria provided, single submitter clinical testing Variant summary: The BRCA2 c.9085G>A (p.Ala3029Thr) variant involves the alteration of a conserved nucleotide and results in a replacement of a small size and hydrophobic Alanine (A) with a medium size and polar Threonine (T). 5/5 in silico tools predict a damaging outcome for this substitution. This variant was found in 6/117622 control chromosomes at a frequency of 0.000051, which does not exceed the estimated maximal expected allele frequency of a pathogenic BRCA2 variant (0.0007503). This variant has been reported in multiple breast and/or ovarian patients; however, without strong evidence for causality. BIC has reported co-occurrence of this variant with pathogenic BRCA1 variants c.5263_5264insC and c.66_67delAG, one in each of the three samples and UMD also reported the variant to co-occur with a BRCA2 splice-site variant c.7436-2A>G, one internally tested individual had a co-occurrence with BRCA1 c.5266dupC. These co-occurrence data strongly suggest the variant to be benign. In support a benign outcome, a likelihood ratio in favor of protein loss of function was calculated to be neutral (Karchin_2008). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign, including two laboratories have classified this variant as benign and likely benign, respectively, since last internal update. Taken together, this variant is classified as benign.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000587355 SCV000887957 benign not provided 2018-08-03 criteria provided, single submitter clinical testing
Color RCV000129046 SCV000902679 likely benign Hereditary cancer-predisposing syndrome 2015-09-09 criteria provided, single submitter clinical testing
Breast Cancer Information Core (BIC) (BRCA2) RCV000114043 SCV000147531 uncertain significance Breast-ovarian cancer, familial 2 2002-05-29 no assertion criteria provided clinical testing
Sharing Clinical Reports Project (SCRP) RCV000114043 SCV000297574 benign Breast-ovarian cancer, familial 2 2008-10-02 no assertion criteria provided clinical testing

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