Starting
Initialising…
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MLH1
Final classification
Uncertain Significance - Conflicting Evidence
MLH1 c.1655C>T · p.Thr552Ile
MLH1

NM_000249.3:c.1655C>T (p.Thr552Ile) is a missense variant in exon 14 of MLH1 that is extremely rare in population databases, observed in 2 of 1,612,688 alleles in gnomAD v4.1 (grpmax filtering AF = 3.65e-06), meeting PM2_Supporting under the InSiGHT MLH1 VCEP v2.0.0.

Gene
MLH1
Transcript
NM_000249.3
HGVS · transcript:coding
NM_000249.3:c.1655C>T
Consequence
N/A
GRCh38
chr3:37040282 C>T
GRCh37
chr3:37081773 C>T
Basis ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MLH1 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 MLH1 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
MLH1 c.1655C>T

NM_000249.3:c.1655C>T (p.Thr552Ile) is a missense variant in exon 14 of MLH1 that is extremely rare in population databases, observed in 2 of 1,612,688 alleles in gnomAD v4.1 (grpmax filtering AF = 3.65e-06), meeting PM2_Supporting under the InSiGHT MLH1 VCEP v2.0.0.1 In silico predictors support a benign computational profile: the MLH1-specific HCI prior probability for pathogenicity is 0.0197, meeting BP4_Supporting (threshold <0.11). SpliceAI predicts no splicing impact (max delta = 0.01). REVEL (0.268) and BayesDel (0.361) are in the indeterminate range.2 This variant has been reported in ClinVar as Uncertain significance by three clinical laboratories (ClinVar Variation ID: 1467499) with no expert panel classification. No publications were identified that specifically report this variant.3 No functional data, segregation data, tumor phenotype data, or de novo observations are available for this variant. Multiple criteria (PS3, PP1, PP4, PS2, BS3, BS4, BS2, BP5) could not be assessed due to absence of evidence. Under the InSiGHT MLH1 VCEP v2.0.0 combining rules, one pathogenic supporting criterion (PM2_Supporting) and one benign supporting criterion (BP4_Supporting) with no other criteria met results in classification as Uncertain Significance — conflicting or insufficient evidence to classify.4

PM2 + BP4 Uncertain Significance - Conflicting Evidence
Gene diagram · NM_000249.3 · variants mapped to exon structure
MLH1 NM_000249.3
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= 1.24017e-06; MAF= 0.00012%, 2/1612688 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 2.19655e-05; MAF= 0.00220%, 2/91052 alleles, homozygotes = 0); grpmax FAF= 3.65e-06.
      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
      0.00012% · 2 / 1,612,688
      0 hom · FAF 0.00037%
      South Asian
      2 / 91,052
      0.0022%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, 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 Uncertain significance (3 clinical laboratories). (ClinVarID = 1467499)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.268. BayesDel score = 0.361201. HCI prior probability for pathogenicity = 0.0197. MAPP score = 4.37. Custom PP2 score = 0.457.
      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. MLH1, a DNA mismatch repair protein, is recurrently altered by deletion and mutation in various cancer types.
      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
      11598466 ↗ Practice parameters for the identification and testing of patients at risk for dominantly inherited colorectal cancer--supporting documentation. CLINVAR
      15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR
      20301390 ↗ Lynch Syndrome. CLINVAR
      22167527 ↗ Identification of individuals at risk for Lynch syndrome using targeted evaluations and genetic testing: National Society of Genetic Counselors and the Collaborative Group of the Americas on Inherited Colorectal Cancer joint practice guideline. CLINVAR
      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