ClinVar Miner

Submissions for variant NM_032043.3(BRIP1):c.2748C>T (p.Tyr916=)

gnomAD frequency: 0.00003  dbSNP: rs555200296
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000166413 SCV000217208 likely benign Hereditary cancer-predisposing syndrome 2014-10-15 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.
GeneDx RCV000431405 SCV000512423 likely benign not specified 2017-08-15 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 RCV000459998 SCV000558569 likely benign Familial cancer of breast; Fanconi anemia complementation group J 2021-12-15 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000431405 SCV000593763 likely benign not specified 2016-11-23 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000166413 SCV000684230 likely benign Hereditary cancer-predisposing syndrome 2016-09-23 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000431405 SCV002014909 benign not specified 2021-10-14 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001357082 SCV001552423 likely benign Malignant tumor of breast no assertion criteria provided clinical testing The BRIP1 p.Tyr916= variant was not identified in the literature nor was it identified in the Cosmic, MutDB, or Zhejiang Colon Cancer Database. The variant was identified in dbSNP (ID: rs555200296) “With Likely benign allele”, ClinVar (classified likely benign by Ambry Genetics, GeneDx, Invitae, Genetic Services Laboratory (University of Chicago) and Color Genomics Inc), Clinvitae (3x), and in control databases in 17 of 277110 chromosomes at a frequency of 0.00006 (Genome Aggregation Database Feb 27, 2017). It was observed in the East Asian population in 17 of 18860 chromosomes (freq: 0.0009); but not in the African, Other, Latino, European Non-Finnish, Ashkenazi Jewish, Finnish, and South Asian populations. The p.Tyr916= 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, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. 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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