ClinVar Miner

Submissions for variant NM_000179.2(MSH6):c.1917G>A (p.Glu639=) (rs368059229)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000162595 SCV000213013 likely benign Hereditary cancer-predisposing syndrome 2015-03-03 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 RCV001081507 SCV000253091 likely benign Hereditary nonpolyposis colorectal neoplasms 2020-12-04 criteria provided, single submitter clinical testing
GeneDx RCV000436098 SCV000513686 benign not specified 2015-03-31 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.
Color Health, Inc RCV000162595 SCV000690236 likely benign Hereditary cancer-predisposing syndrome 2017-08-30 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000588893 SCV000695799 likely benign not provided 2016-04-01 criteria provided, single submitter clinical testing Variant summary: The MSH6 c.1917G>A variant affects a non-conserved nucleotide, resulting in no amino acid change. One in-silico tool predicts damaging outcome for this variant, and 2/5 Alamut algorithms predict a change in a cryptic splice acceptor site. This variant was found in 7/120720 control chromosomes at a frequency of 0.000058, which does not significantly exceed maximal expected frequency of a pathogenic MSH6 allele (0.0001421). However, the variant was predominantly found in East Asians, at an allele frequency of 0.0006935, which is significantly greater than the maximal expected allele frequency, suggesting this may be a benign polymorphism in East Asians. In addition, several clinical laboratories classified this variant as likely benign without evidence to independently evaluate. The variant of interest has not, to our knowledge, been reported in affected individuals via publications, nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant was classified as likely benign until additional information is available.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000588893 SCV001134401 likely benign not provided 2018-10-25 criteria provided, single submitter clinical testing

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