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MSH2
Final classification
VUS
MSH2 c.2001_2002del · p.Thr668TrpfsTer7
MSH2

NM_000251.3:c.2001_2002del is a 2-bp deletion in exon 12 of MSH2 that causes a frameshift (p.Thr668TrpfsTer7) and introduces a premature termination codon at position 674, well before the InSiGHT VCEP PVS1_VeryStrong cutoff of codon 891.

Gene
MSH2
Transcript
NM_000251.3
HGVS · transcript:coding
NM_000251.3:c.2001_2002del
Consequence
N/A
GRCh38
chr2:47475265 TTA>T
GRCh37
chr2:47702404 TTA>T
Basis ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH2 Version 2.0 v2.0 criteria-combination framework was evaluated deterministically with applied criteria: PVS1 very strong, PM2 supporting; no rule matched the adjudicated criteria.
ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH2 Version 2.0 v2.0 criteria-combination framework was evaluated deterministically with applied criteria: PVS1 very strong, PM2 supporting; no rule matched the adjudicated criteria.
Classification rationale
PVS1PM2 VUS
MSH2 c.2001_2002del

NM_000251.3:c.2001_2002del is a 2-bp deletion in exon 12 of MSH2 that causes a frameshift (p.Thr668TrpfsTer7) and introduces a premature termination codon at position 674, well before the InSiGHT VCEP PVS1_VeryStrong cutoff of codon 891.1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2_Supporting under InSiGHT VCEP criteria (allele frequency <0.00002).2 The variant is absent from ClinVar and has not been reported in COSMIC; no published case reports or functional studies specific to this variant were identified in the five publications reviewed.3 Applying the InSiGHT MMR VCEP v2.0 combining rules: one Pathogenic Very Strong criterion (PVS1) plus one Pathogenic Supporting criterion (PM2) meets Rule 10 for Likely Pathogenic (1 Very Strong + 1 Moderate, but PM2 is only Supporting in this VCEP, so the classification defaults to Rule 10: 1 Very Strong + 1 Moderate = Likely Pathogenic; however PM2_Supporting alone with PVS1 does not reach a second moderate — the classification resolves under Rule 1: ≥1 Very Strong = Pathogenic).4

PVS1 + PM2 VUS
4 final_classification_framework
Gene diagram · NM_000251.3 · variants mapped to exon structure
MSH2 NM_000251.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 12 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 very strong Pathogenic
NM_000251.3:c.2001_2002del is a 2-bp deletion in exon 12 of MSH2 causing a frameshift at codon 668 (p.Thr668TrpfsTer7) that introduces a premature termination codon at position 674, well before the InSiGHT VCEP cutoff of codon 891 for PVS1_VeryStrong. The PTC is located >50 nucleotides upstream of the last exon-exon junction and is predicted to trigger nonsense-mediated decay, supporting complete loss of function.
Frameshift variant introduces PTC at codon 674 (NP_000242.1:p.Thr668TrpfsTer7)PTC at codon 674 ≤ VCEP cutoff of codon 891 for MSH2 PVS1_VeryStrongNMD predicted: PTC located >50 nucleotides upstream of last exon-exon junction
PM2 supporting Pathogenic
NM_000251.3:c.2001_2002del is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. The allele frequency is below the InSiGHT VCEP threshold of <0.00002 (<1 in 50,000 alleles) for PM2_Supporting.
Absent from gnomAD v2.1 (0 alleles)Absent from gnomAD v4.1 (0 alleles)Absent from gnomAD-Canada v1.0 (0 alleles)
Assessed · not applied
Pathogenic
PS2 No de novo observations have been reported for this variant.
PS3 This is a frameshift null variant; the InSiGHT VCEP calibrated functional assays (CIMRA, saturation mutagenesis) are designed for missense, splice site, and synonymous variants.
PP1 No co-segregation data available.
PP4 No tumor MSI/IHC data provided.
PP5 This variant is absent from ClinVar.
Benign
BA1 NM_000251.3:c.2001_2002del is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 NM_000251.3:c.2001_2002del is absent from gnomAD v4.1.
BS2 No evidence of co-occurrence in trans with a known pathogenic MSH2 variant in a patient without CMMRD.
BS3 The InSiGHT VCEP BS3 calibrated functional assays target missense, splice site, and synonymous variants.
BS4 No co-segregation data showing lack of segregation with disease.
BP5 No evidence of an alternate molecular basis for disease.
BP6 This variant is absent from ClinVar.
N/A · 13 PS1 · PS4 · PM1 · PM4 · PM5 · PM6 · PP2 · PP3 · BP1 · BP2 · BP3 · BP4 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07).
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 5 PMIDs not cited in assessment
10946232 ↗ Structure and function of mismatch repair proteins. ONCOKB
11257106 ↗ Deficient DNA mismatch repair: a common etiologic factor for colon cancer. ONCOKB
15528792 ↗ Mutations associated with HNPCC predisposition -- Update of ICG-HNPCC/INSiGHT mutation database. ONCOKB
23391514 ↗ Structural, molecular and cellular functions of MSH2 and MSH6 during DNA mismatch repair, damage signaling and other noncanonical activities. ONCOKB
24362816 ↗ Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. ONCOKB