chr2-47429942-G-A
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000251.3(MSH2):c.1276+1G>A variant causes a splice donor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,166 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★).
Frequency
Consequence
NM_000251.3 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461166Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 726918
GnomAD4 genome
ClinVar
Submissions by phenotype
not provided Pathogenic:4Other:1
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PVS1, PM1, PM2_SUP -
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This variant disrupts a canonical splice-donor site and interferes with normal MSH2 mRNA splicing. It has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). In the published literature, the variant has been reported in individuals with hereditary non-polyposis colorectal cancer (HNPCC) (PMID: 19669161 (2010), 15849733 (2005)). This variant has been shown to result in aberrant MSH2 splicing (PMID: 36113988 (2022), 19669161 (2010)). Based on the available information, this variant is classified as pathogenic. -
Lynch syndrome 1 Pathogenic:2
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This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function. -
Lynch syndrome Pathogenic:2
The c.1276+1G>A variant in MSH2 has been reported in at least 2 individuals with Lynch syndrome (Mangold 2005 PMID: 15849733, Betz 2010 PMID: 19669161) and in other clinical laboratories in ClinVar (Variation ID: 90590). It was absent from large population studies. This variant occurs within the canonical splice site (+/- 1,2) and is predicted to cause altered splicing leading to an abnormal or absent protein. In vitro functional studies corroborate this prediction, where PCR on patient RNA has shown to cause aberrant splicing, causes the activation of a cryptic splice site in exon 7 resulting in the in-frame deletion of 16 amino acids in the hMSH3/hMSH6 interaction domain ich is required for proper MSH2 protein function (Betz 2010 PMID: 19669161). In summary, this variant meets criteria to be classified as likely pathogenic for autosomal dominant Lynch syndrome. ACMG/AMP Criteria applied: PS4_Supporting, PM2_Supporting, PP3, PVS1_Strong, PM4. -
Multifactorial likelihood analysis posterior probability >0.99 -
Hereditary cancer-predisposing syndrome Pathogenic:2
This variant causes a G to A nucleotide substitution at the +1 position of intron 7 of the MSH2 gene. RNA studies have shown that this variant causes use of a cryptic site in exon 7 resulting in an in-frame deletion of sixteen amino acids in the MSH6/MSH3 interaction domain. This variant has been reported in individuals affected with Lynch syndrome (PMID: 15849733, 16216036, 19669161). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of MSH2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Likely Pathogenic. -
The c.1276+1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide after coding exon 7 of the MSH2 gene. This mutation has been identified in multiple Lynch syndrome families and shown to cause abnormal splicing (Mangold E et al, Int. J. Cancer 2005 Sep; 116(5):692-702; Betz B et al, J. Cancer Res. Clin. Oncol. 2010 Jan; 136(1):123-34). This mutation has also been identified in at least one proband who met Amsterdam I/II criteria for Lynch syndrome and tumor demonstrated loss of MSH2/MSH6 expression by immunohistochemistry (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In silico splice site analysis predicts that this alteration will weaken the native splice donor site and may result in the creation or strengthening of a novel splice donor site; however, direct evidence is insufficient at this time (Ambry internal data). In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation. -
Carcinoma of colon Pathogenic:1
The c.1276+1G>A variant was identified in 2 of 908 proband chromosomes (frequency: 0.02) from individuals or families with Lynch syndrome (Mangold 2005). The variant was also identified in dbSNP (ID: rs267607950) “With pathogenic, probable-pathogenic allele”, HGMD, “Mismatch Repair Genes Variant Database”, “InSiGHT Colon Cancer Database”, “Zhejiang Colon Cancer Database”, and the “MMR Gene Unclassified Variants Database”. The c.1276+1G>A variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing in all five programs. In a functional study, RT-PCR analysis of the variant allele found that the variant activated a cryptic 5’ splice site in exon 7, resulting in a deletion of 48 nucleotides from this exon, and ultimately an in-frame deletion of 16 amino acids of the hMSH3/hMSH6 interaction domain of the MSH2 protein (Betz 2010). In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -
Hereditary nonpolyposis colon cancer Pathogenic:1
Variant summary: MSH2 c.1276+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. At least two publications report experimental evidence that this variant affects mRNA splicing (Betz_2010, Petersen_2013). The variant was absent in 251052 control chromosomes. c.1276+1G>A has been reported in the literature in multiple individuals affected with Hereditary Nonpolyposis Colorectal Cancer (e.g. Betz_2010, Mangold_2005, Maliaka_1996, Petersen_2013, Kim_2022). These data indicate that the variant is very likely to be associated with disease. Five ClinVar submitters (evaluation after 2014) have classified the variant as pathogenic, and one ClinVar submitter classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Lynch-like syndrome Pathogenic:1
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Hereditary nonpolyposis colorectal neoplasms Pathogenic:1
This sequence change affects a donor splice site in intron 7 of the MSH2 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in the loss of 16 amino acid residue(s), but is expected to preserve the integrity of the reading-frame. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with Lynch syndrome (PMID: 15849733, 19669161, 21520333). It has also been observed to segregate with disease in related individuals. Invitae Evidence Modeling of clinical and family history, age, sex, and reported ancestry of multiple individuals with this MSH2 variant has been performed. This variant is expected to be pathogenic with a positive predictive value of at least 99%. This is a validated machine learning model that incorporates the clinical features of 1,370,736 individuals referred to our laboratory for MSH2 testing. ClinVar contains an entry for this variant (Variation ID: 90590). Studies have shown that disruption of this splice site results in the activation of a cryptic splice site in exon 7 (PMID: 19669161). For these reasons, this variant has been classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at