2-47412411-T-G

Position:

• chr2-47412411-T-G

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 10P and 1B. PM2 PP5_Very_Strong BP4

The NM_000251.3(MSH2):​c.646-3T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MSH2 NM_000251.3 splice_region, intron
• Scores: Splicing: ADA: 0.6133
• Clinical Significance: Pathogenic reviewed by expert panel P:4
• Conservation: PhyloP100: -0.572

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]

MSH2 (HGNC:):

ACMG classification

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 2-47412411-T-G is Pathogenic according to our data. Variant chr2-47412411-T-G is described in ClinVar as [Pathogenic]. Clinvar id is 91162.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr2-47412411-T-G is described in Lovd as [Pathogenic].
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MSH2	NM_000251.3	c.646-3T>G		splice_region_variant, intron_variant		ENST00000233146.7	NP_000242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSH2	ENST00000233146.7	c.646-3T>G		splice_region_variant, intron_variant		1	NM_000251.3	ENSP00000233146.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:4

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Mar 09, 2022	This variant causes a T to G nucleotide substitution at the -3 position of intron 3 of the MSH2 gene. Splicing studies report that this variant causes use of a cryptic splice site in intron 3 and leads to the introduction of a premature stop codon (PMID: 10693791, 11691782). This variant has been reported in individuals affected with or suspected of having Lynch syndrome (PMID: 11691782, 12658575, 16264161). 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. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jan 19, 2023	The c.646-3T>G intronic pathogenic mutation results from a T to G substitution 3 nucleotides upstream from coding exon 4 in the MSH2 gene. This variant (referred to as IVS3-3T>G) has been reported in a family meeting Amsterdam I criteria (Wagner A et al. Am. J. Hum. Genet., 2003 May;72:1088-100). This variant was also identified in one of the first described HNPCC families ("Family G") in 1895 by Dr. Aldred Warthin (Lynch HT et al. Nat. Rev. Cancer, 2015 03;15:181-94). Using diploid-haploid conversion assays, this variant was shown to activate a cryptic acceptor site which results in a transcript containing a 24-base pair intronic insertion at the end of intron 3, introducing a premature stop codon (Yan H et al. Nature, 2000 Feb;403:723-4; Marra G et al. Cancer Res., 2001 Nov;61:7719-21). Functional studies demonstrated no detectable expression of MSH2 and limited expression of MSH6 by Western blotting in hybrid cell lines expressing the variant allele compared to wild type; furthermore, MMR activity for the variant was severely reduced compared to wild type (Marra G et al. Cancer Res., 2001 Nov;61:7719-21). In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site; however, direct evidence is insufficient at this time (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Lynch syndrome Pathogenic:1

Pathogenic, reviewed by expert panel

research

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Sep 05, 2013

Variant causes aberrant splicing leading to truncated protein: full inactivation of variant allele. -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Apr 29, 2021

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Studies have shown that this variant alters MSH2 gene expression and protein function (PMID: 11691782). This variant has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 12658575, 16264161, 11691782,31615790). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 91162). This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 3 of the MSH2 gene. It does not directly change the encoded amino acid sequence of the MSH2 protein. It affects a nucleotide within the consensus splice site of the intron. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	19
DANN	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.61
dbscSNV1_RF	Benign	0.56
SpliceAI score (max)		0.93		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.93		Position offset: 1
DS_AL_spliceai		0.87		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: rs267607930; hg19: chr2-47639550;