ClinVar Genomic variation as it relates to human health

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.

Variant summary: MSH6 c.866_867delinsAA (p.Gly289Glu) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele (comprised of 2 individual constituent variants 2-48025989-C-A and 2-48025988-G-A in cis; GRC37 hg19) was found at a frequency of 8.5e-05 in 282558 control chromosomes, predominantly at a frequency of 0.00019 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 1.34 fold of the estimated maximal expected allele frequency for a pathogenic variant in MSH6 causing Hereditary Nonpolyposis Colorectal Cancer phenotype (0.00014). c.866_867delinsAA has been reported in the literature in individuals affected with HNPCC, colorectal adenomas, colorectal cancer and breast cancer (example, Colley_2005, Devlin_2008, Baglietto_2010, Caminsky_2016). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer/Lynch Syndrome. At-least two co-occurrences with pathogenic variants have been observed internally (APC c.4987G>T, p.Glu1663X; CHEK2 c.1555C>T, p.Arg519X), providing supporting evidence for a benign role. 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: 20028993, 26898890, 16010685, 18269114, 31422818, 26333163, 23621914). ClinVar contains an entry for this variant (Variation ID: 89572). Based on the evidence outlined above, the variant was classified as likely benign.

The p.Gly289Glu variant in MSH6 has been classified as a variant of uncertain si gnificance on September 5, 2013 by the ClinGen-approved InSiGHT Expert Panel (Cl inVar SCV000108262.2). It has been reported in 2 individuals with Lynch syndrome associated tumors (Colley 2005, Devlin 2008) and is present in 4/66588 of Europ ean chromosomes in the Exome Aggregation Consortium database (ExAC, http://exac. broadinstitute.org, note that the ExAC database reports this variant as 2 separa te substitutions in cis, c.866G>A [rs267608079] and c.867C>A [rs267608047]). Com putational prediction tools and conservation analysis are limited or unavailable for this variant. In summary, the clinical significance of the p.Gly289Glu vari ant is uncertain.

The MSH6 c.866_867delinsAA (p.Gly289Glu) variant is absent in gnomAD v2.1.1 (PM2_Supporting). An in silico tool developed for MSH6, CoDP, predicts a benign effect of this variant on protein function (BP4; PMID: 23621914), but this prediction has not been confirmed by functional studies. This variant has been reported in a family with Lynch syndrome (PMID: 20028993), and in individuals with endometrial cancer (PMID: 18269114) and breast cancer (PMID: 26898890). In summary, this variant meets criteria to be classified as of uncertain significance based on the ACMG/AMP criteria: PM2_Supporting, BP4.

This variant is associated with the following publications: (PMID: 26898890, 16010685, 18269114, 23621914, 20028993, 26333163, 26635394)

DNA sequence analysis of the MSH6 gene demonstrated a deletion and insertion of two base pairs in exon 4, c.866_867delinsAA. This in-frame deletion/insertion results in a missense change, p.Gly289Glu. This sequence change has been identified in individuals with colorectal cancer or suspected Lynch syndrome (PMID: 16010685, 20028993, 18269114). This sequence change has been reported in the gnomAD database with a frequency of 0.02% in the non-Finnish European subpopulation (dbSNPs rs368318845, rs267608047 ). The p.Gly289Glu change affects a poorly conserved amino acid residue located in a domain of the MSH6 protein that is known to be functional. The p.Gly289Glu substitution appears to be benign using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD). Due to insufficient evidences and the lack of functional studies, the clinical significance of the p.Gly289Glu change remains unknown at this time.

The p.Gly289Glu variant has been previously reported in the literature in 2/880 proband chromosomes. One individual had multiple colorectal adenomas and the other had HNPCC (Colley 2005, Devlin 2008). However, race-matched population controls were not sequenced in these studies and so it is possible that the full spectrum of benign variation has not yet been defined for this gene, and this variant may be benign. This variant was identified by our laboratory in one individual who had normal IHC for MSH6 and was microsatellite stable increasing the likelihood this variant does not have clinical significance. The p.Gly289 residue is not conserved across mammals and lower species increasing the likelihood that this is a benign variant. In summary, based on the above information, the clinical significance of this variant cannot be determined at this time. Therefore, this variant is classified as a variant of unknown significance.

The MSH6 c.866_867delinsAA variant is predicted to result in an in-frame deletion and insertion. This variant has been reported in several individuals with suspected Lynch syndrome (Devlin et al. 2008. PubMed ID: 18269114; Baglietto et al. 2010. PubMed ID: 20028993; Gordon et al. 2019. PubMed ID: 31422818) and an individual with breast/ovarian cancer (Caminsky et al. 2016. PubMed ID: 26898890). Although this variant is not reported in gnomAD V2.1.1 as c.866_867delinsAA, it is present as two separate variants, c.866G>A and c.867C>A that are found together in 96% and 100% of individuals, respectively, both at a allele frequency of 0.0194% among individuals of European (non-Finnish) descent. The c.866_867delinsAA variant has conflicting interpretations in ClinVar ranging from likely benign to uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/89572/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.