ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.9285C>T (p.Asp3095=) (rs80359198)

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Total submissions: 11
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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) RCV000495427 SCV000578963 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 RCV000164250 SCV000214874 likely benign Hereditary cancer-predisposing syndrome 2015-07-19 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 RCV000206162 SCV000261812 likely benign Hereditary breast and ovarian cancer syndrome 2020-12-01 criteria provided, single submitter clinical testing
Laboratory of Molecular Diagnosis of Cancer,West China Hospital, Sichuan University RCV000240721 SCV000265967 uncertain significance Breast neoplasm 2015-11-01 criteria provided, single submitter research
GeneDx RCV000430642 SCV000512397 benign not specified 2015-08-08 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.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000430642 SCV000600854 uncertain significance not specified 2016-11-03 criteria provided, single submitter clinical testing
Color Health, Inc RCV000164250 SCV000684049 likely benign Hereditary cancer-predisposing syndrome 2017-02-26 criteria provided, single submitter clinical testing
Counsyl RCV000495427 SCV000784922 likely benign Breast-ovarian cancer, familial 2 2017-02-06 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000430642 SCV000919038 likely benign not specified 2019-08-21 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV001311844 SCV001502175 likely benign not provided 2020-10-01 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001354353 SCV001548949 uncertain significance Malignant tumor of breast no assertion criteria provided clinical testing The BRCA2 p.Asp3095= variant was not identified in the literature nor was it identified in the COGR, UMD-LSDB, BIC, ARUP Laboratories, or Zhejiang Colon Cancer databases. The variant was identified in the following databases: dbSNP (ID: rs80359198) as With Pathogenic, Uncertain significance allele, ClinVar (classified as benign by GeneDx; as likely benign by Invitae, Ambry genetics, ENIGMA), Clinvitae (classified as likely benign by ClinVar, Invitae), and LOVD 3.0 (5X). The variant was identified in control databases in 19 of 276410 chromosomes at a frequency of 0.00007; 12 in 18846 East Asians (freq. 0.00064), and 5 of 126212 European Non-Finnish individuals (0.00004) increasing the likelihood that this may be a low frequency variant in certain populations of origin (Genome Aggregation Consortium Feb 27, 2017). The p.Asp3095= 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. However, 3 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this information is not predictive enough to assume pathogenicity. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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