ClinVar Miner

Submissions for variant NM_000179.2(MSH6):c.1050C>T (p.Ala350=) (rs730881802)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000160690 SCV000215047 benign Hereditary cancer-predisposing syndrome 2014-11-18 criteria provided, single submitter clinical testing
Color RCV000160690 SCV000537490 likely benign Hereditary cancer-predisposing syndrome 2015-08-04 criteria provided, single submitter clinical testing
Counsyl RCV000409759 SCV000489426 likely benign Hereditary nonpolyposis colorectal cancer type 5 2016-10-03 criteria provided, single submitter clinical testing
GeneDx RCV000212643 SCV000211311 benign not specified 2014-08-21 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.
Genetic Services Laboratory, University of Chicago RCV000212643 SCV000595840 likely benign not specified 2017-02-16 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000227648 SCV000430957 uncertain significance Lynch syndrome 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586411 SCV000695769 uncertain significance not provided 2017-06-06 criteria provided, single submitter clinical testing Variant summary: The MSH6 c.1050C>T (p.Ala350Ala) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. Mutation taster predicts a disease-causing outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect binding of ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 8/121258 control chromosomes from ExAC, predominantly observed in the European (Non-Finnish) subpopulation at a frequency of 0.00012 (8/66652). This frequency is about slightly lower than the estimated maximal expected allele frequency of a pathogenic MSH6 variant (0.0001421). However, it could still represent a rare benign polymorphism found primarily in the populations of European (Non-Finnish) origin. In ClinVar, while five clinical diagnostic laboratories classified this variant as benign/likely benign, one has classified it as uncertain significance. The variant of interest has not, to our knowledge, been reported in affected individuals via publications. Taken together, this variant is classified as VUS-possibly benign.
Invitae RCV000524099 SCV000283696 likely benign Hereditary nonpolyposis colon cancer 2017-11-16 criteria provided, single submitter clinical testing
PreventionGenetics RCV000586411 SCV000805836 likely benign not provided 2017-10-25 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000212643 SCV000601500 uncertain significance not specified 2017-06-14 criteria provided, single submitter clinical testing

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