MSH6 NM_000179.3:c.942C>G, Ser314Arg

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.

This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 27363726].

Variant summary: MSH6 c.942C>G (p.Ser314Arg) results in a non-conservative amino acid change in the encoded protein sequence. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change. The variant allele was found at a frequency of 4.8e-05 in 251294 control chromosomes, predominantly at a frequency of 0.00068 within the African or African-American subpopulation in the gnomAD database. The observed variant frequency within African or African-American control individuals in the gnomAD database exceeds the estimated maximal expected allele frequency for disease-causing variants in MSH6. c.942C>G has been reported as a germline Benign/VUS variant in settings of multigene panel testing among individuals with a variety of cancers such as ALL, Endometrial and Colorectal Cancer (e.g. Zhang_2015, Ring_2016, Yurgelun_2017). These report(s) do not provide unequivocal conclusions about association of the variant with Lynch Syndrome and related cancers. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 27443514, 28135145, 26580448). ClinVar contains an entry for this variant (Variation ID: 229741). Based on the evidence outlined above, the variant was classified as likely benign.