ClinVar Miner

Submissions for variant NM_000059.4(BRCA2):c.6264T>C (p.Thr2088=)

gnomAD frequency: 0.00001  dbSNP: rs750651726
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Total submissions: 12
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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) RCV000495105 SCV000578942 likely benign Breast-ovarian cancer, familial, susceptibility to, 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/).
Labcorp Genetics (formerly Invitae), Labcorp RCV001083478 SCV000259809 likely benign Hereditary breast ovarian cancer syndrome 2025-01-26 criteria provided, single submitter clinical testing
GeneDx RCV000759638 SCV000519099 likely benign not provided 2020-09-16 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 18844490, 22366370)
Color Diagnostics, LLC DBA Color Health RCV000445816 SCV000537485 likely benign Hereditary cancer-predisposing syndrome 2015-07-22 criteria provided, single submitter clinical testing
Ambry Genetics RCV000445816 SCV000661205 likely benign Hereditary cancer-predisposing syndrome 2015-10-15 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000759638 SCV000889094 likely benign not provided 2020-09-24 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000442483 SCV000916912 likely benign not specified 2019-09-20 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002500644 SCV002809610 likely benign Familial cancer of breast; Breast-ovarian cancer, familial, susceptibility to, 2; Fanconi anemia complementation group D1; Medulloblastoma; Wilms tumor 1; Malignant tumor of prostate; Pancreatic cancer, susceptibility to, 2; Glioma susceptibility 3 2022-03-22 criteria provided, single submitter clinical testing
All of Us Research Program, National Institutes of Health RCV000495105 SCV004846726 likely benign Breast-ovarian cancer, familial, susceptibility to, 2 2023-11-30 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV005235105 SCV005880558 benign Familial cancer of breast 2025-02-01 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV000759638 SCV000592038 likely benign not provided no assertion criteria provided clinical testing The p.Thr2088Thr 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. This variant was identified in the literature by Cvok (2008) in 2 of 115 healthy elderly Croatian women with no family history of cancer. The variant was not identified in any of the databases searched, including dbSNP, UMD, the NHLBI Exome Sequencing Project (Exome Variant Server), HGMD, LOVD, COSMIC, or the BIC database. In silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing; though Cvok (2008) found that an additional program, ESEfinder 3.0, predicted a potential change in splicing motifs. However, these in silico predictions are not very predictive of pathogenicity. 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 predicted benign.
BRCAlab, Lund University RCV000495105 SCV004243706 likely benign Breast-ovarian cancer, familial, susceptibility to, 2 2020-03-02 no assertion criteria provided clinical testing

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