2-47414421-A-T

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PP3_Moderate PP5_Very_Strong

The NM_000251.3(MSH2):c.942+3A>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency:
  • Genomes: 𝑓 0.00070 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0033 (0 hom.)
• Consequence: MSH2 NM_000251.3 splice_donor_region, intron
• Scores: Splicing: ADA: 0.9999
• Clinical Significance: Pathogenic reviewed by expert panel P:28 U:1 O:1
• Conservation: PhyloP100: 2.32

Genes affected

MSH2 (HGNC:7325): (mutS homolog 2) This locus is frequently mutated in hereditary nonpolyposis colon cancer (HNPCC). When cloned, it was discovered to be a human homolog of the E. coli mismatch repair gene mutS, consistent with the characteristic alterations in microsatellite sequences (RER+ phenotype) found in HNPCC. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. Scorers claiming Uncertain: max_spliceai. No scorers claiming Benign.
• PP5: Variant 2-47414421-A-T is Pathogenic according to our data. Variant chr2-47414421-A-T is described in ClinVar as [Pathogenic]. Clinvar id is 36580.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr2-47414421-A-T is described in Lovd as [Pathogenic]. Variant chr2-47414421-A-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSH2	NM_000251.3	c.942+3A>T		splice_donor_region_variant, intron_variant		ENST00000233146.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSH2	ENST00000233146.7	c.942+3A>T		splice_donor_region_variant, intron_variant		1	NM_000251.3	P1

Frequencies

GnomAD3 genomes AF: 0.000699 AC: 2 AN: 2862 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad NFE AF: 0.00244

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000327 AC: 1 AN: 30582 Hom.: 0 AF XY: 0.0000630 AC XY: 1 AN XY: 15866

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000777

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00333 AC: 29 AN: 8714 Hom.: 0 Cov.: 0 AF XY: 0.00392 AC XY: 17 AN XY: 4334

Gnomad4 AFR exome AF: 0.00680

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00385

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00667

Gnomad4 NFE exome AF: 0.00353

Gnomad4 OTH exome AF: 0.00714

GnomAD4 genome AF: 0.000697 AC: 2 AN: 2868 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 1496

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00245

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:28 Uncertain:1 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Lynch syndrome 1 Pathogenic:8 Uncertain:1 Other:1

Pathogenic, no assertion criteria provided	literature only	OMIM	Sep 01, 2000	- -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Mar 24, 2023	This variant is considered pathogenic. Functional studies indicate this variant impacts protein function [PMID: 8062247]. -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 06, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	Jul 28, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Mar 25, 2024	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Nov 17, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	Sep 21, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Apr 12, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	University of Science and Technology Houari Boumediene, Laboratory of Molecular and Cellular Biology (LBCM)	-	- -

not provided Pathogenic:8

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jul 12, 2023	The MSH2 c.942+3A>T variant has been reported in the published literature in several affected individuals with Lynch Syndrome-related cancers (PMIDs: 23329266 (2013), 22949379 (2013), 24323032 (2014), 25117503 (2014), 28874130 (2017), 35734982 (2022), and 36421850 (2022)). A functional study demonstrated that this variant alters normal splicing and results in exon 5 skipping (PMID: 16395668 (2006)). It has also been described as the most common recurrent de novo germline variant in a human mismatch repair gene (PMID: 10978353 (2000)), as well as the most common Lynch Syndrome variant in the world (PMIDs: 20682701 (2010)). The frequency of this variant in the general population, 0.000033 (1/30582 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on splicing yielded predictions that this variant may affect proper MSH2 mRNA splicing. Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Jun 27, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jul 25, 2013	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jan 04, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jan 30, 2023	PP4, PP5, PM2, PS3, PS4_moderate -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 13, 2020	Originally reported to be a pathogenic founder variant in Newfoundland, but has since been hypothesized to be a mutational hotspot identified in individuals of varying ethnicities without a common haplotype identified (Desai 2000); Published functional studies demonstrate a damaging effect: skipping of exon 5 (Liu 1994, Auclair 2006); Observed in individuals with a personal or family history consistent with pathogenic variants in this gene (Liu 1994, Froggatt 1999, Kurzawski 2005, Buchanan 2014, Rosty 2014, Harper 2016, Roth 2016, Ziada-Bouchaar 2016); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 18270343, 10978353, 21598002, 8062247, 27064304, 26873718, 31857677, 25525159, 30702970, 29575718, 29665779, 30680046, 22883484, 25117503, 24323032, 23329266, 21642682, 23255516, 12362047, 19125127, 24603434, 19575290, 18809606, 25479140, 25345868, 10051005, 25648859, 25980754, 21056691, 22775459, 25110875, 20587412, 16395668, 22949379, 21636617, 27013479, 21681552, 26666765, 27468915, 26143115, 27601186, 27978560, 27357288, 27720647, 28243543, 19606495, 18566915, 28152038, 27713421, 28502729, 28514183, 26681312, 28873162, 28577310, 28874130, 29967423, 30093976, 31054147, 30553995, 25795746, 18460031, 31444830, 25025451, 32658311, 31615790, 33484353, 34178123, 31332305, 30875412, 30787465, 33726816) -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 27, 2023	The MSH2 c.942+3A>T variant (rs193922376) is well-described in the literature to be associated with Lynch syndrome and colorectal cancer (Desai 2000, Lage 2004, Liu 1994, Woods 2010, Mismatch Repair Genes Variant Database and references therein). This variant is reported as pathogenic by numerous laboratories in ClinVar (Variation ID: 36580). This is an intronic variant in a moderately conserved nucleotide, and RNA analyses indicate this variant weakens the canonical donor splice site of intron 5 and leads to exon 5 skipping (Auclair 2006, Liu 1994). Based on available information, this variant is considered to be pathogenic. References: Link to Mismatch Repair Genes Variant Database: http://www.med.mun.ca/mmrvariants/search_results.aspx Auclair J et al. Systematic mRNA analysis for the effect of MLH1 and MSH2 missense and silent mutations on aberrant splicing. Hum Mutat. 2006 Feb;27(2):145-54. PMID: 16395668. Desai DC et al. Recurrent germline mutation in MSH2 arises frequently de novo. J Med Genet. 2000 Sep;37(9):646-52. PMID: 10978353. Lage PA et al. Association of colonic and endometrial carcinomas in Portuguese families with hereditary nonpolyposis colorectal carcinoma significantly increases the probability of detecting a pathogenic mutation in mismatch repair genes, primarily the MSH2 gene. Cancer. 2004 Jul 1;101(1):172-7. PMID: 15222003. Liu B et al. hMSH2 mutations in hereditary nonpolyposis colorectal cancer kindreds. Cancer Res. 1994 Sep 1;54(17):4590-4. PMID: 8062247. Woods MO et al. The genetic basis of colorectal cancer in a population-based incident cohort with a high rate of familial disease. Gut. 2010 Oct;59(10):1369-77. PMID: 20682701. -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2023	MSH2: PS3, PS4, PM2, PP1 -

Lynch syndrome Pathogenic:4

Pathogenic, reviewed by expert panel	research	International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	Sep 05, 2013	Multifactorial likelihood analysis posterior probability >0.99. Variant causes in-frame splicing aberration which interrupts know functional domains -
Pathogenic, criteria provided, single submitter	research	A.C.Camargo Cancer Center / LGBM, A.C.Camargo Cancer Center	Jan 30, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	May 08, 2019	The c.942+3A>T variant in MSH2 has been reported in >150 individuals with Lynch syndrome (LabCorp database, Woods 2010). This variant has been identified in 1/12862 of European chromosomes by gnomAD (https://gnomad.broadinstitute.org/). In vitro functional studies show that the c.942+3A>T variant leads to an in-frame deletion of exon 5 (Auclair 2006). In addition, it has been classified as Pathogenic on December 18, 2013 by the ClinGen-approved InSiGHT expert panel (ClinVar SCV000107794.2). In summary, this variant meets criteria to be classified as pathogenic for Lynch syndrome in an autosomal dominant manner based upon the predicted impact to the protein, low frequency in controls and presence in affected individuals. ACMG/AMP Criteria applied: PS4, PM2, PS3_Supporting, PVS1_Strong. -
Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Jan 08, 2024	This variant causes an A to T nucleotide substitution at the +3 position of intron 5 of the MSH2 gene. RNA studies have shown this variant caused skipping of exon 5 (r.793_942del) and in-frame deletion of 50 amino acids in the DNA binding domain (PMID: 8062247, 16395668, 19267393). This variant has been reported as a recurrent de novo mutation in individuals affected with Lynch syndrome-associated cancer in different ethnicities (PMID: 10978353). This variant has been reported in many individuals and families with Lynch syndrome or suspected Lynch syndrome worldwide (PMID: 8062247, 10413423, 10446963, 11920650, 12112654, 12362047, 15222003, 16203774, 16395668, 17312306, 18625694, 19130300, 19419416, 20682701, 21681552, 22883484), and shown to segregate with Lynch syndrome cancers in family studies (PMID: 19267393). This variant is considered to be a founder mutation in the Newfoundland population (PMID: 20682701). This variant has been identified in 1/30582 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Feb 22, 2023	This variant causes an A to T nucleotide substitution at the +3 position of intron 5 of the MSH2 gene. RNA studies have shown this variant caused skipping of exon 5 (r.793_942del) and in-frame deletion of 50 amino acids in the DNA binding domain (PMID: 8062247, 16395668, 19267393). This variant has been reported as a recurrent de novo mutation in individuals affected with Lynch syndrome-associated cancer in different ethnicities (PMID: 10978353). This variant has been reported in many individuals and families with Lynch syndrome or suspected Lynch syndrome worldwide (PMID: 8062247, 10413423, 10446963, 11920650, 12112654, 12362047, 15222003, 16203774, 16395668, 17312306, 18625694, 19130300, 19419416, 20682701, 21681552, 22883484), and shown to segregate with Lynch syndrome cancers in family studies (PMID: 19267393). This variant is considered to be a founder mutation in the Newfoundland population (PMID: 20682701). This variant has been identified in 1/30582 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Mar 09, 2022	The c.942+3A>T intronic pathogenic mutation results from an A to T substitution 3 nucleotides after coding exon 5 in the MSH2 gene. In one study, this mutation was found in eight unrelated Lynch syndrome families. Six of the eight families (75%) had one family member diagnosed with either a keratocanthoma or sebaceous adenoma associated with Muir-Torre syndrome, along with some combination of colon, uterine, and/or ureter transitional cell cancers in the family (South CD et al. J. Natl. Cancer Inst. 2008 Feb;100:277-81). This mutation was also reported in a German patient diagnosed with malignant fibrous histiocytoma (MFH) (Brieger A et al. Fam. Cancer. 2011 Sep;10:591-5). Authors of one study claim that this is the most common recurrent de novo germline mutation in a human mismatch repair gene, accounting for approximately 11% of all known pathogenic MSH2 gene mutations (Desai DC et al. J. Med. Genet. 2000 Sep;37:646-52). Multiple studies have demonstrated that this mutation results in an mRNA transcript lacking coding exon 5 (Casey G et al. JAMA. 2005 Feb;293:799-809; Auclair J et al. Hum. Mutat. 2006 Feb;27:145-54; Arnold S et al. Hum. Mutat. 2009 May;30:757-70; Chong G et al. Hum. Mutat. 2009 Aug;30:E797-812). Of note, this mutation is also designated as IVS5+3A>T in published literature. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Pathogenic, criteria provided, single submitter	curation	Sema4, Sema4	Mar 10, 2021	- -

Carcinoma of colon Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The MSH2 c.942+3A>T variant was identified in 12 of 2642 proband chromosomes (frequency: 0.005) from individuals or families with colorectal cancer, and was not identified in 200 control chromosomes from healthy individuals (Auclair 2006, Brieger 2011, Canard 2012, Froggatt 1996, Grindedal 2009, Kurzawski 2002, Sheng 2008). The variant was also identified by our laboratory in 8 individuals with colorectal cancer. The variant was identified in dbSNP (ID: rs193922376) as “With Pathogenic allele”, Clinvitae database (as pathogenic), “Mismatch Repair Genes Variant Database”, InSiGHT Colon Cancer Gene Variant Database (LOVD), Zhejiang Colon Cancer Database (LOVD), ClinVar database (classified as pathogenic by InSight, Emory Genetics, Ambry genetics, Invitae, LabCorp, COGR, Mayo Clinic, GeneDx, OMIM) and UMD (111X with a “causal” classification). The c.942+3A>T variant is located at the donor splice site (or 3’ splice site of exon 5) but does not affect the invariant +1 and +2 positions. However, positions +3 to +6 are part of the splicing consensus sequence and variants involving these positions sometimes affect splicing. In addition, 5 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. Furthermore, several population studies suggest the variant lead to an in-frame deletion of exon 5 and loss of MSH2 protein expression (Auclair 2006, Brieger 2011, Canard 2012, Kurzawski 2002). 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

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Sep 08, 2021

Variant summary: MSH2 c.942+3A>T alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: two predict the variant abolishes a 5 prime splicing donor site; two predict the variant weakens a 5 prime splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing (Liu_1994). The variant allele was found at a frequency of 3.3e-05 in 30582 control chromosomes. c.942+3A>T has been reported in the literature in multiple individuals affected with Hereditary Nonpolyposis Colorectal Cancer (Liu_1994, Thibodeau_1996, Chan_1999, Desai_2000, Green_2002, Win_2011). These data indicate that the variant is very likely to be associated with disease. Fourteen clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Lynch-like syndrome Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Constitutional Genetics Lab, Leon Berard Cancer Center

Jul 01, 2019

- -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jan 22, 2024

This sequence change falls in intron 5 of the MSH2 gene. It does not directly change the encoded amino acid sequence of the MSH2 protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 8062247, 10978353, 15222003, 19419416, 20682701, 21681552, 22883484, 24310308). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 36580). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of 5, but is expected to preserve the integrity of the reading-frame (PMID: 8062247, 16395668; Invitae). For these reasons, this variant has been classified as Pathogenic. -

Breast carcinoma Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Medical Genetics Laboratory, Umraniye Training and Research Hospital, University of Health Sciences

Aug 21, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
Cadd	Benign	16
Dann	Benign	0.94

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.99
SpliceAI score (max)		0.49		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.49		Position offset: -3

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs193922376; hg19: chr2-47641560; COSMIC: COSV51881499; COSMIC: COSV51881499;