MSH2 c.645+2T>A, p.Splice_Site
NM_000251.3:c.645+2T>A
Pathogenic
This canonical +2 splice donor variant in MSH2 is absent from population databases and is predicted to abolish normal splicing leading to NMD (PVS1 Very Strong, PM2 Supporting). Under VCEP classification rules, PVS1 plus an additional criterion is sufficient for Pathogenic.
ACMG/AMP Criteria Applied
PVS1
PM2
Genetic Information
Gene & Transcript Details
Gene
MSH2
Transcript
NM_000251.3
MANE Select
Total Exons
16
Strand
Forward (+)
Reference Sequence
NC_000002.11
Alternative Transcripts
| ID | Status | Details |
|---|---|---|
| NM_000251.2 | RefSeq Select | 16 exons | Forward |
| NM_000251.1 | Alternative | 16 exons | Forward |
Variant Details
HGVS Notation
NM_000251.3:c.645+2T>A
Protein Change
Splice
Location
Exon 3
(Exon 3 of 16)
5'Exon Structure (16 total)3'
Functional Consequence
Loss of Function
Related Variants
Variant interpretation based on transcript NM_000251.3
Genome Browser
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HGVS InputNM_000251:c.645+2T>A
Active Tracks
ConservationRefSeqClinVargnomAD
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Clinical Data
Population Frequency
Global Frequency
0.0 in 100,000
Extremely Rare
Global: 0.0%
0%
0.05%
0.1%
1%
5%
10%+
ACMG Criteria Applied
PM2
This variant is not present in gnomAD (PM2 criteria applies).
Classification
1 publications
Likely Pathogenic
Based on 1 submitter review in ClinVar
Submitter Breakdown
1 LP
Pathogenic
Likely Path.
VUS
Likely Benign
Benign
Publications (1)
This sequence change affects a donor splice site in intron 3 of the MSH2 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with MSH2-related conditions. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in MSH2 are known to be pathogenic (PMID: 15849733, 24362816). 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.
Clinical Statement
This variant has been reported in ClinVar as Likely pathogenic (1 clinical laboratories).
Functional Impact
Functional Domain
Hotspot Status
Not a hotspot
Domain Summary
This variant is not located in a mutational hotspot or critical domain (0 mutations).
Related Variants in This Domain
Computational Analysis
Pathogenicity Predictions
Predictor Consensus
Mixed/VUS
PP3 Applied
No
Additional Predictors
Benign:
CADD: 5.50
VCEP Guidelines
Applied ACMG/AMP Criteria (VCEP Specific) VCEP Guidelines
PVS1
PVS1 (Very Strong)
According to VCEP guidelines, the rule for PVS1 Very Strong is: 'Variants at IVS±1 or IVS±2 a,c where exon skipping or use of a cryptic splice site disrupts reading frame and is predicted to undergo NMD.' The evidence shows this variant is at the +2 splice donor site in MSH2 and is predicted to abolish normal splicing leading to a premature termination codon and NMD. Therefore, this criterion is applied at Very Strong strength because it meets the VCEP requirement for a canonical splice site variant predicted to undergo NMD.
PS1
PS1 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for PS1 Strong is: 'A predicted missense substitution that encodes the same amino acid change with a different underlying nucleotide change previously established as Pathogenic.' This variant is a splice donor change, not a missense encoding the same amino acid. Therefore, this criterion is not applied.
PS2
PS2 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for PS2 Very Strong/Strong/Moderate/Supporting relates to de novo occurrence with parental confirmation. There is no de novo evidence for this variant. Therefore, this criterion is not applied.
PS3
PS3 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for PS3 Strong is: 'Calibrated functional assays with functional odds for Pathogenicity > 18.7.' There are no functional assay data available for this variant. Therefore, this criterion is not applied.
PS4
PS4 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for PS4 Strong is: 'The prevalence of the variant in affected individuals is significantly increased compared to controls.' No case-control or segregation data meeting PS4 criteria are available. Therefore, this criterion is not applied.
PM1
PM1 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for PM1 Moderate is: 'Located in a mutational hot spot and/or critical functional domain without benign variation.' This variant affects a splice site and not a protein domain. Therefore, this criterion is not applied.
PM2
PM2 (Supporting) Strength Modified
According to VCEP guidelines, the rule for PM2 Supporting is: 'Absent/extremely rare (<1 in 50,000 alleles) in gnomAD v4 dataset.' The variant is absent from gnomAD. Therefore, this criterion is applied at Supporting strength because it meets the VCEP requirement for extremely low population frequency.
PM3
PM3 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for PM3 relates to observation in trans with a pathogenic variant in recessive disorders. No such evidence is available for this variant in MSH2. Therefore, this criterion is not applied.
PM4
PM4 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for PM4 Moderate is: 'Protein length changes due to in‐frame deletions/insertions in a non‐repeat region or stop‐loss variants.' This is a splice site variant, not an in‐frame indel. Therefore, this criterion is not applied.
PM5
PM5 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for PM5 Moderate is: 'Missense change at an amino acid residue where a different missense change was classified as Pathogenic.' This variant does not encode a missense change. Therefore, this criterion is not applied.
PM6
PM6 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for PM6 Supporting is: 'Assumed de novo without confirmation of paternity and maternity.' There is no de novo information. Therefore, this criterion is not applied.
PP1
PP1 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for PP1 relates to segregation data. No segregation data are available. Therefore, this criterion is not applied.
PP2
PP2 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for PP2 Supporting is: 'Missense variant in a gene with low rate of benign missense variants.' This is a canonical splice site variant. Therefore, this criterion is not applied.
PP3
PP3 (Not Applied) Strength Modified
According to VCEP guidelines, PVS1 at IVS±1 or ±2 is not to be combined with PP3 for confirmed splice defect. Therefore, this criterion is not applied despite splicing predictions.
PP4
PP4 (Not Applied) Strength Modified
According to VCEP guidelines, the rule for PP4 relates to tumor phenotype and MMR deficiency. No tumor or MSI data are provided. Therefore, this criterion is not applied.
PP5
PP5 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for PP5 Supporting is: 'Reputable source reports variant as pathogenic but evidence not available.' While ClinVar lists Likely Pathogenic, primary evidence is available and evaluated directly. Therefore, this criterion is not applied.
BA1
BA1 (Not Applied) Strength Modified
According to VCEP guidelines, BA1 requires a high population frequency ≥0.1%. The variant is absent from population databases. Therefore, this criterion is not applied.
BS1
BS1 (Not Applied) Strength Modified
According to VCEP guidelines, BS1 requires a population frequency between 0.01–0.1%. The variant is absent. Therefore, this criterion is not applied.
BS2
BS2 (Not Applied) Strength Modified
According to VCEP guidelines, BS2 relates to benign co‐occurrence in trans in Lynch syndrome genes. No such data are available. Therefore, this criterion is not applied.
BS3
BS3 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for BS3 Strong is: 'Well‐established functional studies show no damaging effect.' No functional assays demonstrate benign impact. Therefore, this criterion is not applied.
BS4
BS4 (Not Applied) Strength Modified
According to standard ACMG guidelines, the rule for BS4 Strong is: 'Lack of segregation in affected members.' No segregation evidence is available. Therefore, this criterion is not applied.
BP1
BP1 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP1 Supporting applies to missense in a gene where only truncating variants cause disease. This is a splice variant. Therefore, this criterion is not applied.
BP2
BP2 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP2 Supporting is: 'Observed in trans with a pathogenic variant for a fully penetrant dominant gene.' Not applicable. Therefore, this criterion is not applied.
BP3
BP3 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP3 Supporting is: 'In-frame indels in repetitive regions.' Not applicable to this splice variant. Therefore, this criterion is not applied.
BP4
BP4 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP4 Supporting is: 'Computational evidence supports no impact.' SpliceAI predicts high impact. Therefore, this criterion is not applied.
BP5
BP5 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP5 Strong/Supporting relates to variant found in a case with an alternative molecular basis. No such data. Therefore, this criterion is not applied.
BP6
BP6 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP6 Supporting is: 'Reputable source reports benign but evidence not available.' No such benign reports. Therefore, this criterion is not applied.
BP7
BP7 (Not Applied) Strength Modified
According to standard ACMG guidelines, BP7 Supporting is: 'Synonymous or intronic beyond −21/+7 with no splicing impact.' This is a canonical splice site variant. Therefore, this criterion is not applied.