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MSH6
Final classification
VUS
MSH6 c.440T>G · p.Leu147Arg
MSH6

NM_000179.2:c.440T>G (p.Leu147Arg) is a missense variant in exon 2 of MSH6.

Gene
MSH6
Transcript
NM_000179.2
HGVS · transcript:coding
NM_000179.2:c.440T>G
Consequence
N/A
GRCh38
chr2:47791106 T>G
GRCh37
chr2:48018245 T>G
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 was evaluated deterministically with applied criteria: 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 MSH6 Version 2.0.0 v2.0.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting; no rule matched the adjudicated criteria.
Classification rationale
PM2 VUS
MSH6 c.440T>G

NM_000179.2:c.440T>G (p.Leu147Arg) is a missense variant in exon 2 of MSH6. This variant is extremely rare in population databases, observed in 1 of 1,614,050 alleles in gnomAD v4.1 (AF = 6.20e-07), meeting PM2_Supporting under the InSiGHT MSH6 VCEP framework.1 The variant is classified as Uncertain Significance in ClinVar by 3 clinical laboratories (ClinVar Variation ID: 1740396) with no expert panel submissions.2 No variant-specific functional studies, cosegregation data, de novo observations, or tumor phenotype data were identified in the VCEP functional assay documentation, ClinVar submissions, or published literature.3 In silico predictors are inconclusive: HCI prior probability is 0.3529 (below PP3 thresholds), REVEL score is 0.222, BayesDel is -0.269843, and SpliceAI predicts no splicing impact (delta = 0.01). These do not meet thresholds for PP3 or BP4 under the VCEP framework.4 No same-residue pathogenic comparator variant (PM5) or same-amino-acid nucleotide change comparator (PS1) was identified in the VCEP pilot variants.5 With only PM2_Supporting met, and no benign or additional pathogenic criteria fulfilled, the variant is classified as Uncertain Significance under the InSiGHT MSH6 VCEP v2.0.0 combination rules.6

PM2 VUS
3 vcep_functional_assay_svi_documentation_mmroncokb ↗
4 hci_priorrevelbayesdelspliceai ↗
5 vcep_vcep_pilot_variants_mmrpm5_candidates
6 cspec ↗final_classification_framework
Gene diagram · NM_000179.2 · variants mapped to exon structure
MSH6 NM_000179.2
Fetching transcript structure from UCSC…
Applied criteria · 1 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= 6.19559e-07; MAF= 0.00006%, 1/1614050 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 1.33465e-05; MAF= 0.00133%, 1/74926 alleles, homozygotes = 0).
      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
      6.2e-05% · 1 / 1,614,050
      0 hom
      African/African American
      1 / 74,926
      0.0013%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, 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 Uncertain significance (3 clinical laboratories). (ClinVarID = 1740396)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.222. BayesDel score = -0.269843. HCI prior probability for pathogenicity = 0.3529. MAPP score = 24.22. Custom PP2 score = 0.319.
      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 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 · 6 PMIDs not cited in assessment
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      20301390 ↗ Lynch Syndrome. CLINVAR
      24493721 ↗ American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers. CLINVAR
      34012068 ↗ ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG). CLINVAR
      24905773 ↗ Endometrial cancer: a review and current management strategies: part I. CLINVAR
      24929052 ↗ Endometrial cancer: a review and current management strategies: part II. CLINVAR