Submissions for variant NM_000251.3(MSH2):c.1276+1G>A

dbSNP: rs267607950

Total submissions: 15

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000076086	SCV000107101	pathogenic	Lynch syndrome	2013-09-05	reviewed by expert panel	research	Multifactorial likelihood analysis posterior probability >0.99
Ambry Genetics	RCV000491508	SCV000580472	pathogenic	Hereditary cancer-predisposing syndrome	2020-05-04	criteria provided, single submitter	clinical testing	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.
Invitae	RCV000548164	SCV000625246	pathogenic	Hereditary nonpolyposis colorectal neoplasms	2023-01-28	criteria provided, single submitter	clinical testing	For these reasons, this variant has been classified as Pathogenic. Studies have shown that disruption of this splice site results in the activation of a cryptic splice site in exon 7 (PMID: 19669161). ClinVar contains an entry for this variant (Variation ID: 90590). 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. This variant is not present in population databases (gnomAD no frequency). 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.
Color Diagnostics, LLC DBA Color Health	RCV000491508	SCV000684922	likely pathogenic	Hereditary cancer-predisposing syndrome	2022-03-29	criteria provided, single submitter	clinical testing	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.
CeGaT Center for Human Genetics Tuebingen	RCV000786795	SCV001249232	pathogenic	not provided	2021-07-01	criteria provided, single submitter	clinical testing
Genetics and Molecular Pathology, SA Pathology	RCV002272053	SCV002556768	pathogenic	Lynch syndrome 1	2021-06-22	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV002469005	SCV002765982	pathogenic	Hereditary nonpolyposis colon cancer	2022-11-25	criteria provided, single submitter	clinical testing	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.
Revvity Omics, Revvity	RCV000786795	SCV003822161	pathogenic	not provided	2022-11-21	criteria provided, single submitter	clinical testing
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	RCV000786795	SCV004026074	pathogenic	not provided	2022-07-01	criteria provided, single submitter	clinical testing	PVS1, PM1, PM2_SUP
Myriad Genetics, Inc.	RCV002272053	SCV004186701	likely pathogenic	Lynch syndrome 1	2023-08-01	criteria provided, single submitter	clinical testing	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.
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000786795	SCV004220943	pathogenic	not provided	2022-12-16	criteria provided, single submitter	clinical testing	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.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000076086	SCV004848540	likely pathogenic	Lynch syndrome	2021-10-27	criteria provided, single submitter	clinical testing	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.
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001353592	SCV000592495	pathogenic	Carcinoma of colon		no assertion criteria provided	clinical testing	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.
MutSpliceDB: a database of splice sites variants effects on splicing, NIH	RCV000786795	SCV000925685	not provided	not provided		no assertion provided	in vitro
Constitutional Genetics Lab, Leon Berard Cancer Center	RCV001250019	SCV001423944	pathogenic	Lynch-like syndrome	2019-07-01	no assertion criteria provided	clinical testing