Starting
Initialising…
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MSH2
Final classification
VUS
MSH2 c.198C>A · p.Tyr66Ter
MSH2

PVS1_VeryStrong is met: c.198C>A (p.Tyr66Ter) is a nonsense variant introducing a premature termination codon at codon 66, which is ≤ codon 891 in MSH2, satisfying the InSiGHT MSH2 v2.0.0 VCEP PVS1 rule for full-strength PVS1.

Gene
MSH2
Transcript
NM_000251.3
HGVS · transcript:coding
NM_000251.3:c.198C>A
Consequence
N/A
GRCh38
chr2:47403389 C>A
GRCh37
chr2:47630528 C>A
Basis Richards et.al., 2015 - Combining rules v2.0.0 criteria-combination framework was evaluated deterministically with applied criteria: PVS1 very strong, PM2 supporting; no rule matched the adjudicated criteria.
Richards et.al., 2015 - Combining rules v2.0.0 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.198C>A

PVS1_VeryStrong is met: c.198C>A (p.Tyr66Ter) is a nonsense variant introducing a premature termination codon at codon 66, which is ≤ codon 891 in MSH2, satisfying the InSiGHT MSH2 v2.0.0 VCEP PVS1 rule for full-strength PVS1.1 PM2_Supporting is met: the variant is absent from gnomAD v4.1 (0/1,601,554 alleles) and gnomAD v2.1, satisfying the VCEP PM2_Supporting threshold of <0.00002 (<1 in 50,000 alleles).2 Under the InSiGHT MSH2 v2.0.0 VCEP combination rules (Richards et al. 2015 framework), the combination of 1 Pathogenic Very Strong (PVS1) and 1 Pathogenic Supporting (PM2) does not satisfy any rule for Pathogenic or Likely Pathogenic classification. A minimum of 1 Very Strong + 2 Supporting, or 1 Very Strong + 1 Moderate would be required for Pathogenic or Likely Pathogenic, respectively. The variant is classified as Variant of Uncertain Significance (VUS) per the VCEP combination rule set.3 This variant has been reported as Pathogenic by 6 clinical laboratories in ClinVar (VariationID: 645593). However, the VCEP does not recognize PP5/ClinVar consensus as an applicable criterion, and no expert panel classification has been issued for this variant.4 No variant-specific functional (PS3/BS3), segregation (PP1/BS4), tumor phenotype (PP4/BP5), or de novo (PS2) data were identified for this variant in any reviewed source. Full-text publications retrieved for relevant PMIDs (24362816, 10946232, 11257106, 15528792, 23391514) did not contain accessible article content — all returned Sci-Hub landing page artifacts without variant-specific evidence.

PVS1 + PM2 VUS
1 cspec ↗pvs1_variant_assessmentpvs1_gene_context
Gene diagram · NM_000251.3 · variants mapped to exon structure
MSH2 NM_000251.3
Fetching transcript structure from UCSC…
Applied criteria · 2 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 0; MAF= 0.00000%, 0/1601554 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/74900 alleles, homozygotes = 0).
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / 1,601,554
      0 hom
      Not observed in any ancestry group.
      + 10 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
      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 has been reported in ClinVar as Pathogenic (6 clinical laboratories). (ClinVarID = 645593)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). BayesDel score = 0.66.
      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
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 8 PMIDs not cited in assessment
      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
      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
      7726159 ↗ Seven new mutations in hMSH2, an HNPCC gene, identified by denaturing gradient-gel electrophoresis. ONCOKB
      8566964 ↗ CpG dinucleotides in the hMSH2 and hMLH1 genes are hotspots for HNPCC mutations. ONCOKB
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR