ClinVar Miner

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

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Total submissions: 10
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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; http://priors.hci.utah.edu/PRIORS/).
Ambry Genetics RCV000165865 SCV000216614 likely benign Hereditary cancer-predisposing syndrome 2014-09-08 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Invitae RCV001081793 SCV000253006 likely benign Hereditary breast and ovarian cancer syndrome 2020-12-03 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.
Color Health, Inc 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
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000430864 SCV000918834 likely benign not specified 2021-07-23 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000430864 SCV001160453 benign not specified 2019-04-06 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000759593 SCV001501464 likely benign not provided 2020-10-01 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001353444 SCV000591827 likely benign Malignant tumor of breast no assertion criteria provided clinical testing The BRCA2 p.Thr939= variant was identified in 1 of 3050 proband chromosomes (frequency: 0.0003) from individuals or families with breast cancer (Caux-Moncoutier 2011). The variant was also identified in dbSNP (ID: rs367921107) as With Likely benign allele, ClinVar (classified as benign by GeneDx; classified as likely benign by ENIGMA, Ambry Genetics, Invitae), Clinvitae, LOVD 3.0 (2X), UMD-LSDB (13X as unclassified variant), databases. The variant was not identified in BIC Database, ARUP Laboratories, Zhejiang Colon Cancer Database, databases. The variant was identified in control databases in 13 of 245704 chromosomes at a frequency of 0.000053 (Genome Aggregation Consortium Feb 27, 2017). The p.Thr939= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, the variant was identified with a co-occurring pathogenic BRCA2 variant (c.8488-1G>A), increasing the likelihood that the c.2817C>T variant does not have clinical significance (Santos 2014). In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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