ClinVar Miner

Submissions for variant NM_000059.3(BRCA2):c.2786T>C (p.Leu929Ser) (rs2227943)

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Total submissions: 19
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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) RCV000077285 SCV000244432 benign Breast-ovarian cancer, familial 2 2015-08-10 reviewed by expert panel curation IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 1 based on posterior probability = 0.0000741
Invitae RCV000167848 SCV000072068 benign Hereditary breast and ovarian cancer syndrome 2020-12-04 criteria provided, single submitter clinical testing
GeneDx RCV000120345 SCV000167346 benign not specified 2013-10-08 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.
Michigan Medical Genetics Laboratories,University of Michigan RCV000077285 SCV000195970 benign Breast-ovarian cancer, familial 2 2014-11-03 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000120345 SCV000202280 benign not specified 2014-02-17 criteria provided, single submitter clinical testing
Ambry Genetics RCV000162622 SCV000213057 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.
Counsyl RCV000077285 SCV000220279 benign Breast-ovarian cancer, familial 2 2014-04-29 criteria provided, single submitter literature only
Illumina Clinical Services Laboratory,Illumina RCV000077285 SCV000383657 likely benign Breast-ovarian cancer, familial 2 2018-02-02 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.
Illumina Clinical Services Laboratory,Illumina RCV000299643 SCV000383658 likely benign Fanconi anemia, complementation group D1 2018-02-02 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000167848 SCV000494312 benign Hereditary breast and ovarian cancer syndrome 2014-03-04 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001283408 SCV000602853 benign none provided 2020-08-08 criteria provided, single submitter clinical testing
Color Health, Inc RCV000162622 SCV000683500 benign Hereditary cancer-predisposing syndrome 2015-09-30 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000120345 SCV000805676 benign not specified 2016-11-02 criteria provided, single submitter clinical testing
Research and Development, ARUP Laboratories RCV001646101 SCV001854733 benign Breast-ovarian cancer, familial 2; Breast-ovarian cancer, familial 1; Hereditary breast and ovarian cancer syndrome 2020-01-20 criteria provided, single submitter curation
ITMI RCV000120345 SCV000084497 not provided not specified 2013-09-19 no assertion provided reference population
Sharing Clinical Reports Project (SCRP) RCV000077285 SCV000109082 benign Breast-ovarian cancer, familial 2 2012-05-01 no assertion criteria provided clinical testing
Breast Cancer Information Core (BIC) (BRCA2) RCV000077285 SCV000146107 benign Breast-ovarian cancer, familial 2 2002-05-29 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001353953 SCV000591823 benign Malignant tumor of breast no assertion criteria provided clinical testing The p.Leu929Ser variant was identified in the BIC database 41X and in the UMD database and indicated as either having no clinical significance or as being neutral, respectively. This variant is not conserved in mammals and lower organisms, although computational analysis (SIFT, AlignGVGD, BLOSUM) disagree on whether or not this variant may impact the protein. However, this information is not informative. The variant was identified in the dbSNP database (ID: rs2227943) in the HapMap-Yoruban cohort with a frequency of 0.022 and in the exome variant server database as having with a frequency of 0.004 in the African American cohort, increasing the likelihood this variant does not have clinical significance. Furthermore, Myriad genetics calls this variant as a "polymorphism" increasing the likelihood this variant does not have clinical significance. In summary, this variant meets our laboratory's criteria to be classfied as benign.
Mayo Clinic Laboratories, Mayo Clinic RCV000656593 SCV000778655 benign not provided 2018-02-28 no assertion criteria provided clinical testing

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