ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.90T>C (p.Asn30=) (rs760655471)

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Total submissions: 6
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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) RCV000495762 SCV000578852 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/).
Ambry Genetics RCV000163143 SCV000213660 likely benign Hereditary cancer-predisposing syndrome 2014-12-03 criteria provided, single submitter clinical testing
GeneDx RCV000427494 SCV000518439 likely benign not specified 2018-01-08 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.
Invitae RCV000459050 SCV000560404 likely benign not provided 2019-01-29 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000427494 SCV000600841 likely benign not specified 2016-08-19 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000427494 SCV000695209 likely benign not specified 2019-04-16 criteria provided, single submitter clinical testing Variant summary: BRCA2 c.90T>C alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 2.2e-05 in 275792 control chromosomes (gnomAD and publication). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance.To our knowledge, no occurrence of c.90T>C in individuals affected with Hereditary Breast and Ovarian Cancer and no experimental evidence demonstrating its impact on protein function have been reported. Four ClinVar submissions from clinical diagnostic laboratories and an expert panel (ENIGMA) (evaluation after 2014) cite the variant as likely benign. Based on the evidence outlined above, the variant was classified as likely benign.

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