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MSH6
Final classification
Uncertain Significance - Conflicting Evidence
MSH6 c.188C>T · p.Ser63Phe
MSH6

NM_000179.2:c.188C>T (p.Ser63Phe) is a missense variant in MSH6 exon 1. The variant is extremely rare, observed in 1 of 1,509,420 alleles (AF = 6.625e-07) in gnomAD v4.1 and absent from gnomAD v2.1, meeting PM2_Supporting under the InSiGHT MSH6 VCEP v2.0.0 framework.

Gene
MSH6
Transcript
NM_000179.2
HGVS · transcript:coding
NM_000179.2:c.188C>T
Consequence
N/A
GRCh38
chr2:47783421 C>T
GRCh37
chr2:48010560 C>T
Basis ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH6 Version 2.0.0 v2.0.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP4 supporting benign; maps to Uncertain Significance - Conflicting Evidence.
ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH6 Version 2.0.0 v2.0.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP4 supporting benign; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PM2 BP4 Uncertain Significance - Conflicting Evidence
MSH6 c.188C>T

NM_000179.2:c.188C>T (p.Ser63Phe) is a missense variant in MSH6 exon 1. The variant is extremely rare, observed in 1 of 1,509,420 alleles (AF = 6.625e-07) in gnomAD v4.1 and absent from gnomAD v2.1, meeting PM2_Supporting under the InSiGHT MSH6 VCEP v2.0.0 framework.1 Multiple in silico predictors are consistent with a benign effect. The HCI prior probability for p.Ser63Phe is 0.003, meeting BP4_Supporting (threshold < 0.11). REVEL score is 0.195, BayesDel score is -0.269, and SpliceAI predicts no splicing impact (max delta = 0.00).2 PVS1 is not applicable (missense variant). PS1 is not met (no alternate nucleotide change encoding p.Ser63Phe classified as P/LP by this VCEP). PM5 is not met because PP3 is not supporting (HCI prior 0.003, far below PP3_Supporting threshold of >0.68). Multiple VCEP criteria are explicitly Not Applicable: PS4, PP5, PM1, PM6, PP2, BP1, BP2, BP6.3 The variant has been reported in ClinVar as Uncertain significance by two clinical laboratories (VariationID: 1053294). It has been observed in somatic cancers (COSMIC COSV52275784, n = 6). No variant-specific functional data, segregation data, de novo occurrences, or tumor phenotype data were identified.4 At present, the only scored criteria are PM2_Supporting (pathogenic) and BP4_Supporting (benign), which offset. Multiple criteria remain unassessed due to absence of clinical, functional, and segregation data. Comprehensive assessment awaits functional assay results for p.Ser63Phe, tumor MSI/IHC data from variant carriers, and segregation analysis.

PM2 + BP4 Uncertain Significance - Conflicting Evidence
Gene diagram · NM_000179.2 · variants mapped to exon structure
MSH6 NM_000179.2
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= 6.62506e-07; MAF= 0.00007%, 1/1509420 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.84159e-07; MAF= 0.00009%, 1/1131018 alleles, homozygotes = 0).
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Not available in gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      6.6e-05% · 1 / 1,509,420
      0 hom
      European (non-Finnish)
      1 / 1,131,018
      8.8e-05%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      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 Uncertain significance (2 clinical laboratories). (ClinVarID = 1053294)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.195. BayesDel score = -0.269383. HCI prior probability for pathogenicity = 0.003. Custom PP2 score = 0.027.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. MSH6, a DNA mismatch repair protein, is frequently mutated in colorectal, small bowel, and endometrial cancers.
      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 previously been reported in somatic cancers (COSMIC; COSV52275784, n = 6 times).
      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 · 2 PMIDs not cited in assessment
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR