2-47783394-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBP6_Very_Strong
The NM_000179.3(MSH6):c.161G>C(p.Gly54Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000546 in 1,574,636 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★★).
Frequency
Consequence
NM_000179.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000283 AC: 5AN: 176940Hom.: 0 AF XY: 0.0000408 AC XY: 4AN XY: 98060
GnomAD4 exome AF: 0.0000591 AC: 84AN: 1422346Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 38AN XY: 704704
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74458
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:2Benign:2
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. -
BP4, BP5 c.161G>C located in exon 1 of the MSH6 gene, is predicted to result in the substitution of glycine by alanine at codon 54; p.(Gly54Ala). This variant is found in 84/1160400 with a filter allele frequency of 0.005% in the gnomAD v4.1.0 database (European Non-Finnish data set). Computational tools for this variant suggests no significant impact on splicing (SpliceAI) or protein function (MAPP+PolyPhen-2 prior probability for pathogenicity: 0.001) (BP4). It has been reported in two patients with colorectal cancer samples sowing conserved MSH6 expression (PMID:14520694 and internal data) (BP5). To our knowledge, functional studies have not been reported for this variant. In addition, the variant has been reported in ClinVar (4x uncertain significance, 5x likely benign, 3x benign), LOVD (1x uncertain significance, 1x likely benign) and in the InSiGHT database as Class 2: likely not pathogenic (multifactorial likelihood analysis posterior probability 0.001-0.049). Based on currently available information, the variant c.161G>C is classified as a likely benign variant according to ClinGen-CRC_ACMG_Specifications_MSH6_v1.0.0. -
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This missense variant replaces glycine with alanine at codon 54 of the MSH6 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individual affected with colorectal cancer, whose tumor data demonstrated normal expression of MLH1, MSH2, and MSH6 protein via immunohistochemistry (PMID: 14520694). This variant has been identified in 5/176940 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Lynch syndrome 5 Benign:3
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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: 25085752]. -
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not specified Uncertain:1Benign:1
Variant summary: MSH6 c.161G>C (p.Gly54Ala) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 2.8e-05 in 176940 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.161G>C has been reported in the literature in one individual affected with Colorectal Cancer with positive MSH6 on IHC and MSS tumor (Peterlongo_2003) as well as in patients with breast/ovarian cancer without strong evidence for causality (Pal_2012, Tung_2014). These data do not allow any conclusion about variant significance. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Eight ClinVar submitters have assessed the variant since 2014: five have classified the variant as likely benign, two as benign, and one as of uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. -
The p.Gly54Ala variant in MSH6 has been reported in 1 individuals with colorectal cancer (Peterlongo 2013) and in 1 individual with ovarian cancer (Pal 2012). It has also been identified in 4/72210 of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant was classified as Likely benign on September 5, 2013 by the ClinGen-approved InSiGHT expert panel (Variation ID 89208). Computational prediction tools and conservation analysis suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity (Ali 2012, Terui 2013). In vivo functional studies provide some evidence that this variant does not impact protein function (Peterlong 2013). In summary, the p.Gly54Ala variant is classified as Likely Benign. ACMG/AMP criteria applied: BS3, BP4. -
not provided Uncertain:1Benign:1
In the published literature, this variant has been identified in individuals with ovarian cancer and colorectal cancer (PMIDs: 14520694 (2003), 23047549 (2012)). Internal laboratory indicates that this variant was observed with a pathogenic variant in the MUTYH gene, suggesting that this variant may not be the primary cause of disease. The frequency of this variant in the general population, 0.000055 (4/72210 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded conflicting predictions that this variant is disease causing or benign. Based on the available information, we are unable to determine the clinical significance of this variant. -
This variant is associated with the following publications: (PMID: 14520694, 23047549, 22290698, 23621914, 24933000, 26332594) -
Breast and/or ovarian cancer Uncertain:1
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Lynch syndrome Benign:1
Multifactorial likelihood analysis posterior probability 0.001-0.049 -
Hereditary nonpolyposis colorectal neoplasms Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at