ClinVar Miner

Submissions for variant NM_000179.2(MSH6):c.3488A>T (p.Glu1163Val) (rs63750252)

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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) RCV000074868 SCV000108080 likely benign Lynch syndrome 2013-09-05 reviewed by expert panel research MAF >1% in specific population
GeneDx RCV000121587 SCV000170363 benign not specified 2014-02-18 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 RCV000132123 SCV000187191 benign Hereditary cancer-predisposing syndrome 2014-11-18 criteria provided, single submitter clinical testing
Invitae RCV000524178 SCV000260303 benign Hereditary nonpolyposis colon cancer 2018-01-09 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000121587 SCV000539699 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: Lik Ben by expert panel
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000121587 SCV000592645 benign not specified 2016-02-10 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000121587 SCV000601574 likely benign not specified 2017-03-03 criteria provided, single submitter clinical testing
Color RCV000132123 SCV000685410 benign Hereditary cancer-predisposing syndrome 2014-12-09 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587729 SCV000695870 benign not provided 2016-06-01 criteria provided, single submitter clinical testing Variant summary: The MSH6 c.3488A>T (p.Glu1163Val) variant involves the alteration of a conserved nucleotide. 3/5 in silico tools predict a damaging outcome. This variant was found in 148/121590 control chromosomes, predominantly observed in the East Asian subpopulation at a frequency of 0.0137604 (119/8648). This frequency is about 97 times the estimated maximal expected allele frequency of a pathogenic MSH6 variant (0.0001421), suggesting this is likely a benign polymorphism found primarily in the populations of East Asian origin. It was also reported in HNPCC patients, however without strong evidence for pathogenicity such as co-segregation of the variant with the disease in affected family members. Additionally, databases and multiple clinical diagnostic laboratories classify variant as Benign/Likely benign. Considering the high prevalence of the variant in the East Asian population, it was classified as Benign.
PreventionGenetics,PreventionGenetics RCV000121587 SCV000805893 benign not specified 2016-11-02 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000587729 SCV000888276 benign not provided 2018-03-10 criteria provided, single submitter clinical testing
ITMI RCV000121587 SCV000085783 not provided not specified 2013-09-19 no assertion provided reference population
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic RCV000121587 SCV000257259 uncertain significance not specified no assertion criteria provided research

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