ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.2817C>T (p.Thr939=) (rs367921107)

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Total submissions: 9
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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) RCV000494816 SCV000578881 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;
Ambry Genetics RCV000165865 SCV000216614 likely benign Hereditary cancer-predisposing syndrome 2014-09-08 criteria provided, single submitter clinical testing
Invitae RCV001081793 SCV000253006 likely benign Hereditary breast and ovarian cancer syndrome 2019-12-31 criteria provided, single submitter clinical testing
GeneDx RCV000430864 SCV000512351 benign not specified 2015-07-06 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.
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000430864 SCV000591827 likely benign not specified 2014-08-20 criteria provided, single submitter clinical testing
Color RCV000165865 SCV000683503 benign Hereditary cancer-predisposing syndrome 2016-07-04 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000759593 SCV000889012 benign not provided 2017-11-15 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000430864 SCV000918834 likely benign not specified 2017-09-19 criteria provided, single submitter clinical testing Variant summary: The BRCA2 c.2817C>T (p.Thr939Thr) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. Mutation taster predicts a benign outcome for this variant. 3/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE site of SF2/ASF and SRp40. However, these predictions have yet to be confirmed by functional studies. This variant was found in 13/245704 control chromosomes, predominantly observed in the Latino subpopulation at a frequency of 0.000269 (9/33504). This frequency is only about 2.7 fold lower than the estimated maximal expected allele frequency of a pathogenic BRCA2 variant (0.0007503), suggesting this is possibly a rare benign polymorphism found primarily in the populations of Latino origin. The variant has been observed in a breast cancer patient along with a likely pathogenic BRCA2 variant (c.8488-1G>A; Santos_2014) suggesting this variant is not the cause of breast cancer in this patient. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Taken together, this variant is classified as Likely Benign, until additional information is available.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000430864 SCV001160453 benign not specified 2019-04-06 criteria provided, single submitter clinical testing

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