2-47482929-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PVS1_ModerateBP6_Strong
The NM_000251.3(MSH2):c.2785C>T(p.Arg929*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000348 in 1,611,374 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★★).
Frequency
Consequence
NM_000251.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.000105 AC: 16AN: 151974Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000845 AC: 21AN: 248568Hom.: 0 AF XY: 0.0000594 AC XY: 8AN XY: 134568
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1459282Hom.: 0 Cov.: 31 AF XY: 0.0000262 AC XY: 19AN XY: 725822
GnomAD4 genome 0.000105 AC: 16AN: 152092Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74364
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:1Benign:2
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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. -
Lynch syndrome 1 Uncertain:2
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not provided Uncertain:1Benign:1
Nonsense variant predicted to result in protein truncation as the last 6 amino acids are lost, although loss-of-function variants have not been reported downstream of this position in the protein; Occurred in cis with a nonsense variant in the MSH6 gene in eight unrelated Portuguese Lynch syndrome families; tumor immunohistochemistry (IHC) revealed normal MSH2 expression in 5/8 cases and absence of MSH6 protein in 7/7 cases with interpretable data (PMID: 26446363); Observed in two individuals with colorectal cancer, co-occurring with a pathogenic MSH2 founder pathogenic variant in one individual, as well as in individuals with breast and/or ovarian cancer (PMID: 12624141, 21681552, 24240112, 26824983, 28050010, 28724667, 32068069, 35264596, 35449176, 35534704); This variant is associated with the following publications: (PMID: 12624141, 28127413, 28724667, 21681552, 24344984, 24240112, 26824983, 28874130, 28332257, 29752822, 29506494, 28050010, 9774676, 18822302, 21120944, 27873144, 33015532, 31569399, 26689913, 32029870, 31207149, 35264596, 35980532, 32068069, 35534704, 28514183, 26446363, 35449176) -
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not specified Benign:2
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Variant summary: MSH2 c.2785C>T (p.Arg929X) results in a premature termination codon, predicted to cause a truncation of the encoded protein. This variant leads to encoding a protein that is 6 AA shorter and without interruption of any known functional domain (Pinto_MSH2_JHG_2016). Truncations downstream of this position have not been classified as pathogenic by our laboratory or in ClinVar. The variant allele was found at a frequency of 8.4e-05 in 248768 control chromosomes, predominantly at a frequency of 0.00093 within the East Asian subpopulation in the gnomAD database. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 1.64 fold of the estimated maximal expected allele frequency for a pathogenic variant in MSH2 causing Hereditary Nonpolyposis Colorectal Cancer phenotype (0.00057), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. c.2785C>T has been reported in the literature in individuals affected with colorectal cancer, lynch syndrome, breast cancer, and prostate cancer (examples: Parc_2003, Valentin_2011, Feliubadalo_2017, Lin_2016, Pennington_2013, Pinto_2016, Lu_2015, Sun_2017, Li_2019, Kwong_2020, Fang_2023). However, many of these cases had one or more co-occurrences with other pathogenic variants (MSH2 c. 942+3A>T; MSH6 c.1030C>T, p.Gln344Ter; BRCA1 c.190T>C, p.C64R; BRCA2 c.9090dupA, p.T3030fs; BRCA1 c.4327C>T, p.R1443X) (Valentin_2011, Pinto_2016, Sun2017 and Li_2019 ), providing supporting evidence for a benign role. These reports do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer. The following publications have been ascertained in the context of this evaluation (PMID: 16451135, 28127413, 24344984, 36522531, 28050010, 32068069, 29752822, 26824983, 26689913, 12624141, 24240112, 26446363, 28724667, 21681552). 11 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Multiple submitters reported the variant with conflicting assessments - pathogenic (n=1), likely benign/benign (n=4) and VUS (n=6). Based on the evidence outlined above, the variant was classified as likely benign. -
Gastric cancer Pathogenic:1
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Carcinoma of colon Uncertain:1
The p.Arg989X variant was identified in 10 of 474 proband chromosomes (frequency: 0.021) from South American and Portugese individuals or families with Lynch syndrome, meeting Amsterdam or Bethesda criteria, and was not identified in 200 control chromosomes from healthy individuals (Valentin 2011, Pinto 2015). However eight of the nine patients identified by Pinto et al. were also found to have a co-occurring pathogenic MSH6 mutation (c.1030C>T, p.Gln344X), five of the eight double mutant tumors had normal MSH2 expression and the ninth patient lacked a family history of colon cancer. The patient identified by Valentin et al. was also found to have a co-occurring pathogenic mutation, MSH2: c.942+3A>T (Valentin 2011). The variant was also identified in dbSNP (ID: rs551060742) “With pathogenic allele”, 1000 Genomes Project in 1 of 5000 chromosomes (frequency: 0.0002), the Exome Aggregation Consortium (ExAC) database (released Jan 13, 2015) in 9 of 113840 chromosomes (frequency: 0.00008) (or 9 individuals from a population of 8454 East Asian individuals, frequency 0.001); Clinvitae database (classification pathogenic), InSiGHT Colon Cancer Gene Variant Database (LOVD), ClinVar database (classified as pathogenic, and reviewed by an expert panel; being classified as pathogenic by InSight, and uncertain significance by Invitae), and UMD (9x with a “causal” classification). The above classifications were only updated as recently as 2014. The variant was also identified by our laboratory in 1 individual of Portugese background, with colon cancer, co-occurring with a pathogenic MSH6 mutation (c.1030C>T, p.Gln344X), as seen in the Portugese families from Pinto’s study (Pinto_2015_26446363). The p.Arg989X variant leads to a premature stop codon at position 989, which is predicted to lead to a truncated or absent protein and loss of function. Loss of function variants of the MSH2 gene are an established mechanism of disease in Lynch syndrome and this is the type of variant expected to cause the disorder. However, the p.Arg989X encodes a protein 6 amino acids short of the wildtype transcript, without interruption of any known functional domain. Notably, this mutation occurs in the last exon of the MSH2 gene and stop codon or nonsense mutations in this region may not be subjected to nonsense mediated RNA decay. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. However, due to conflicting interpretations above, this variant is classified as a variant of unknown significance. -
Lynch syndrome Uncertain:1
Nonsense variant after codon 888 in MSH2 = VUS -
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