ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.6412G>T (p.Val2138Phe) (rs11571659)

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Total submissions: 21
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000044938 SCV000072951 benign Hereditary breast and ovarian cancer syndrome 2020-12-07 criteria provided, single submitter clinical testing
Counsyl RCV000077373 SCV000154066 benign Breast-ovarian cancer, familial 2 2014-01-21 criteria provided, single submitter literature only
Ambry Genetics RCV000128955 SCV000172835 benign Hereditary cancer-predisposing syndrome 2014-11-19 criteria provided, single submitter clinical testing This alteration is classified as 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.
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000120342 SCV000225183 benign not specified 2014-08-04 criteria provided, single submitter clinical testing
Michigan Medical Genetics Laboratories,University of Michigan RCV000077373 SCV000267796 benign Breast-ovarian cancer, familial 2 2016-04-21 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000311226 SCV000383744 likely benign Fanconi anemia, complementation group D1 2018-09-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Illumina Clinical Services Laboratory,Illumina RCV000077373 SCV000383745 likely benign Breast-ovarian cancer, familial 2 2018-09-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
A.C.Camargo Cancer Center / LGBM, A.C.Camargo Cancer Center RCV000414271 SCV000492498 uncertain significance Breast neoplasm criteria provided, single submitter research
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000044938 SCV000494338 benign Hereditary breast and ovarian cancer syndrome 2014-09-29 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000120342 SCV000602798 benign not specified 2019-03-06 criteria provided, single submitter clinical testing
Color Health, Inc RCV000128955 SCV000683781 likely benign Hereditary cancer-predisposing syndrome 2015-03-10 criteria provided, single submitter clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000077373 SCV000744492 likely benign Breast-ovarian cancer, familial 2 2015-09-21 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000120342 SCV000805743 benign not specified 2017-03-20 criteria provided, single submitter clinical testing
ITMI RCV000120342 SCV000084494 not provided not specified 2013-09-19 no assertion provided reference population
Sharing Clinical Reports Project (SCRP) RCV000077373 SCV000109170 benign Breast-ovarian cancer, familial 2 2012-05-01 no assertion criteria provided clinical testing
Breast Cancer Information Core (BIC) (BRCA2) RCV000077373 SCV000146846 uncertain significance Breast-ovarian cancer, familial 2 2002-05-29 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000120342 SCV000592049 benign not specified no assertion criteria provided clinical testing The p.Val2138Phe variant has been identified in 4 out of 4579 proband chromosomes (frequency 0.001) in individuals with unilateral, contralateral and familial breast cancer phenotype, and also found in 1 out of 190 control chromosomes (frequency 0.005) included in these studies (Wagner 1999, Capanu 2011, Thesis (South African)). It is listed in dbSNP database coming from a “clinical source” (ID#: rs11571659) with a “global minor allele frequency of 0.001 (1000 genomes), therefore increasing the likelihood that this variant is benign. This residue is not highly conserved in mammals and computational analyses (PolyPhen, SIFT, AlignGVGD) do not suggest a high likelihood of impact to the protein. In the UMD database, this variant has been identified in 1 (out of 5) individuals with breast or ovarian cancers, where a second pathogenic BRCA1 mutation was also detected, further suggesting that this is a benign variant. In addition, Myriad genetics has reported this variant as a polymorphism increasing the likelihood this variant is benign (personal communication). In summary, based on above information this variant is classified as Benign.
Mayo Clinic Laboratories, Mayo Clinic RCV000656613 SCV000778698 likely benign not provided 2018-02-01 no assertion criteria provided clinical testing
Clinical Genetics Laboratory, Department of Pathology,Netherlands Cancer Institute RCV000120342 SCV001906324 benign not specified no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000656613 SCV001930621 likely benign not provided no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000656613 SCV001953967 likely benign not provided no assertion criteria provided clinical testing

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