ClinVar Miner

Submissions for variant NM_000179.3(MSH6):c.3300G>A (p.Thr1100=)

gnomAD frequency: 0.00001  dbSNP: rs540252208
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000164766 SCV000215442 likely benign Hereditary cancer-predisposing syndrome 2014-07-11 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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.
GeneDx RCV000443070 SCV000513698 benign not specified 2015-08-04 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.
Invitae RCV001087767 SCV000624842 likely benign Hereditary nonpolyposis colorectal neoplasms 2024-01-10 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000164766 SCV000685386 likely benign Hereditary cancer-predisposing syndrome 2016-05-22 criteria provided, single submitter clinical testing
University of Washington Department of Laboratory Medicine, University of Washington RCV000758625 SCV000887382 likely benign Lynch syndrome 2018-05-01 criteria provided, single submitter clinical testing MSH6 NM_000179.2:c.3300G>A has a 1.6% probability of pathogenicity based on combining prior probability from public data with likelihood ratios of 1.56 and 0.20 to 1, generated from evidence of seeing this as a somatic mutation in two independent tumors without loss of heterozygosity at the MSH6 locus. See Shirts et al 2018, PMID 29887214.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000759142 SCV000888271 benign not provided 2018-08-23 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000759142 SCV000892560 likely benign not provided 2018-08-01 criteria provided, single submitter clinical testing
Mendelics RCV000986733 SCV001135837 likely benign Lynch syndrome 5 2019-05-28 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000164766 SCV002528007 likely benign Hereditary cancer-predisposing syndrome 2021-01-01 criteria provided, single submitter curation
PreventionGenetics, part of Exact Sciences RCV004535103 SCV004714129 likely benign MSH6-related disorder 2021-02-05 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
All of Us Research Program, National Institutes of Health RCV000758625 SCV004835042 likely benign Lynch syndrome 2023-12-01 criteria provided, single submitter clinical testing

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