ClinVar Miner

Submissions for variant NM_000179.2(MSH6):c.-18G>T (rs199913053)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000132459 SCV000187553 likely benign Hereditary cancer-predisposing syndrome 2019-01-18 criteria provided, single submitter clinical testing Other strong data supporting benign classification;Subpopulation frequency in support of benign classification
GeneDx RCV000212623 SCV000211372 benign not specified 2014-06-17 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 RCV000132459 SCV000910595 likely benign Hereditary cancer-predisposing syndrome 2015-05-18 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000212623 SCV000917759 benign not specified 2018-04-13 criteria provided, single submitter clinical testing Variant summary: MSH6 c.-18G>T is located in the untranslated mRNA region upstream of the initiation codon. The variant was observed with an allele frequency of 0.0003 in 270744 control chromosomes (gnomAD). The observed variant frequency is approximately 2-folds higher than the estimated maximal expected allele frequency for a pathogenic variant in MSH6 causing Lynch Syndrome phenotype (0.00014), strongly suggesting that the variant is benign. The variant, c.-18G>T, has been reported in the literature in an individual affected with Lynch Syndrome (Lamberti_2006). These report(s) do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. A ClinVar submission from a clinical diagnostic laboratory (evaluation after 2014) cites the variant as "likely benign." Based on the evidence outlined above, the variant was classified as benign.

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