ClinVar Miner

Submissions for variant NM_000059.4(BRCA2):c.2350A>G (p.Met784Val) (rs11571653)

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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) RCV000113034 SCV000245024 benign Breast-ovarian cancer, familial 2 2015-01-12 reviewed by expert panel curation Class 1 not pathogenic based on frequency >1% in an outbred sampleset. Frequency 0.02797 (Asian), derived from 1000 genomes (2012-04-30).
Invitae RCV000195303 SCV000071990 benign Hereditary breast and ovarian cancer syndrome 2020-12-07 criteria provided, single submitter clinical testing
GeneDx RCV000120314 SCV000167342 benign not specified 2013-10-03 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.
Ambry Genetics RCV000131146 SCV000186086 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 RCV000113034 SCV000220807 benign Breast-ovarian cancer, familial 2 2014-10-16 criteria provided, single submitter literature only
Illumina Clinical Services Laboratory,Illumina RCV000270154 SCV000383649 likely benign Fanconi anemia, complementation group D1 2017-04-27 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 RCV000113034 SCV000383650 likely benign Breast-ovarian cancer, familial 2 2017-04-27 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 RCV000412901 SCV000492493 uncertain significance Breast neoplasm criteria provided, single submitter research
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000120314 SCV000538471 likely benign not specified 2016-03-28 criteria provided, single submitter clinical testing Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ClinVar: Ben by expert panel
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000034435 SCV000883509 benign not provided 2017-10-09 criteria provided, single submitter clinical testing
Color Health, Inc RCV000131146 SCV000910571 benign Hereditary cancer-predisposing syndrome 2015-10-29 criteria provided, single submitter clinical testing
Mendelics RCV000113034 SCV001139028 benign Breast-ovarian cancer, familial 2 2019-05-28 criteria provided, single submitter clinical testing
Research and Development, ARUP Laboratories RCV001642539 SCV001854719 uncertain significance Breast-ovarian cancer, familial 2; Breast-ovarian cancer, familial 1; Hereditary breast and ovarian cancer syndrome 2020-01-20 criteria provided, single submitter curation
Biesecker Lab/Clinical Genomics Section,National Institutes of Health RCV000034435 SCV000043203 no known pathogenicity not provided 2012-07-13 no assertion criteria provided research Converted during submission to Benign.
ITMI RCV000120314 SCV000084466 not provided not specified 2013-09-19 no assertion provided reference population
Breast Cancer Information Core (BIC) (BRCA2) RCV000113034 SCV000146033 uncertain significance Breast-ovarian cancer, familial 2 2002-05-29 no assertion criteria provided clinical testing
Sharing Clinical Reports Project (SCRP) RCV000113034 SCV000189299 benign Breast-ovarian cancer, familial 2 2011-03-10 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001353474 SCV000591802 benign Malignant tumor of breast no assertion criteria provided clinical testing The p.Met784Val variant has been reported in the literature in 160/11460 proband chromosomes of individuals with HBOC and sporadic breast cancer. It was also found in 35/5936 control chromosomes tested, increasing the likelihood this variant does not have clinical significance (Spearman 2008, Wagner 1999, Capanu 2011, Freedman_2004, Ishitobi_2003, Johnston_2012, Krupa_2009, Seo_2004, Han_2006). The variant has also been reported in the UMD (x1), LOVD (x2), BIC (x47), and BOCs databases. It is listed in the dbSNP database as coming from a "clinical source" (ID#: rs11571653) with a MAF score of 0.007 (1000 Genomes). Of particular interest are the findings that this variant is considered a polymorphism in the Japanese population, and that of the 168 chromosomes tested in the HapMap Japanese cohort, the variant was found in almost 20 chromosomes (allele frequency of 0.107). The p.Met784 residue is not conserved in mammals, and the variant amino acid Valine (Val) is present in the dog, rat and opossum at this position, increasing the likelihood that an alteration to this residue may not have functional significance. The identification of this variant in the presence of a second pathogenic variant increases the likelihood that this variant does not have clinical significance. In summary, based on the above information, this variant is classified as Benign.
True Health Diagnostics RCV000131146 SCV000787924 likely benign Hereditary cancer-predisposing syndrome 2018-02-15 no assertion criteria provided clinical testing

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