ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.9411T>G (p.Thr3137=) (rs1799968)

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Total submissions: 7
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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) RCV000494944 SCV000578020 benign Breast-ovarian cancer, familial 2 2017-06-29 reviewed by expert panel curation Synonymous substitution variant, with low bioinformatic likelihood to alter mRNA splicing (splicing prior 0.02; http://priors.hci.utah.edu/PRIORS/) and frequency 0.0033 (Finnish), derived from ExAC (2014-12-17).
Ambry Genetics RCV000163082 SCV000213585 likely benign Hereditary cancer-predisposing syndrome 2014-11-20 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 RCV001082585 SCV000253060 benign Hereditary breast and ovarian cancer syndrome 2020-11-13 criteria provided, single submitter clinical testing
GeneDx RCV000588721 SCV000516027 likely benign not provided 2021-09-07 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 10399947, 9150152, 9585608, 20104584)
Color Health, Inc RCV000163082 SCV000689194 likely benign Hereditary cancer-predisposing syndrome 2017-01-13 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000588721 SCV000695238 benign not provided 2016-05-18 criteria provided, single submitter clinical testing Variant summary: The BRCA2 c.9411T>G (p.Thr3137Thr) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant, and 4/5 Alamut algorithms predict no significant change to splicing. This variant was found in 63/121504 control chromosomes, predominantly observed in the ExAC European (Finnish) subpopulation at a frequency of 0.0033303 (22/6606). This frequency is about 4 times the estimated maximal expected allele frequency of a pathogenic BRCA2 variant (0.0007503), suggesting this is likely a benign polymorphism found primarily in the populations of European (Finnish) origin. This variant has also been detected mainly in Finnish cancer patients from the literature, but without evidence of causality. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign. Taken together, this variant is classified as benign.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001287804 SCV001474534 likely benign none provided 2019-08-30 criteria provided, single submitter clinical testing

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