Starting
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MLH3
Final classification
VUS
MLH3 c.3637G>A · p.Glu1213Lys
MLH3

NM_001040108.2:c.3637G>A (p.Glu1213Lys) is a missense variant in exon 6 of MLH3, a mismatch repair gene associated with Lynch syndrome and polyposis predisposition.

Gene
MLH3
Transcript
NM_001040108.2
HGVS · transcript:coding
NM_001040108.2:c.3637G>A
Consequence
N/A
GRCh38
chr14:75038346 C>T
GRCh37
chr14:75505049 C>T
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BP4 supporting benign; combination = 1 supporting benign, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: BP4 supporting benign; combination = 1 supporting benign, which maps to VUS.
Classification rationale
BP4 VUS
MLH3 c.3637G>A

NM_001040108.2:c.3637G>A (p.Glu1213Lys) is a missense variant in exon 6 of MLH3, a mismatch repair gene associated with Lynch syndrome and polyposis predisposition.1 This variant is present in gnomAD population databases at low frequency: v2.1 AF=0.0113% (32/282,848 alleles) and v4.1 AF=0.0144% (232/1,612,714 alleles), with no homozygotes observed. It does not meet BA1 (>1%), BS1 (>0.3%), or PM2 (absent/extremely low) population frequency thresholds.2 ClinVar reports this variant as Uncertain Significance based on submissions from 5 clinical laboratories (ClinVar variation ID 847280). No expert panel review or pathogenic classification is available.3 Multiple in silico predictors concordantly suggest a benign effect: REVEL score 0.068, BayesDel score -0.421, and SpliceAI max delta 0.04, supporting BP4 (supporting benign).4 No variant-specific functional studies, segregation data, de novo occurrences, case-control enrichment, or pathogenic comparator variants at the same residue were identified. No publications specifically mention this variant. The only met criterion is BP4 (supporting benign). No pathogenic or other benign criteria are met. The evidence is insufficient to classify this variant beyond Uncertain Significance under generic ACMG/AMP 2015 rules.5

BP4 VUS
1 pvs1_variant_assessment
4 revelbayesdelspliceai ↗
5 generic_acmg_combination_rules
Gene diagram · NM_001040108.2 · variants mapped to exon structure
MLH3 NM_001040108.2
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= 0.000143857; MAF= 0.01439%, 232/1612714 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 0.000312705; MAF= 0.03127%, 20/63958 alleles, homozygotes = 0); grpmax FAF= 0.00015121.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.000113135; MAF= 0.01131%, 32/282848 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.000276778; MAF= 0.02768%, 2/7226 alleles, homozygotes = 0); grpmax FAF= 0.00013731.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.014% · 232 / 1,612,714
      0 hom · FAF 0.015%
      European (Finnish)
      20 / 63,958
      0.031%
      European (non-Finnish)
      201 / 1,178,786
      0.017%
      Remaining individuals
      4 / 62,460
      0.0064%
      African/African American
      4 / 75,002
      0.0053%
      Ashkenazi Jewish
      1 / 29,592
      0.0034%
      Admixed American
      1 / 60,022
      0.0017%
      South Asian
      1 / 91,044
      0.0011%
      + 3 not observed (Amish, East Asian, Middle Eastern)
      gnomAD v2.1
      0.011% · 32 / 282,848
      0 hom · FAF 0.014%
      Remaining individuals
      2 / 7,226
      0.028%
      European (Finnish)
      5 / 25,088
      0.02%
      European (non-Finnish)
      24 / 129,196
      0.019%
      African/African American
      1 / 24,964
      0.004%
      + 4 not observed (Admixed American, Ashkenazi Jewish, East Asian, South Asian)
      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 (5 clinical laboratories). (ClinVarID = 847280)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04). REVEL score = 0.068. BayesDel score = -0.421174.
      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. MLH3, a DNA mismatch repair protein, is infrequently altered in cancer.
      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
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 11 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
      26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
      26389505 ↗ Genetics of Colorectal Cancer (PDQ®): Health Professional Version. CLINVAR
      33451724 ↗ Endometrial cancer: A society of gynecologic oncology evidence-based review and recommendations, part II. CLINVAR
      33516529 ↗ Endometrial cancer: A society of gynecologic oncology evidence-based review and recommendations. CLINVAR
      34043773 ↗ European guidelines from the EHTG and ESCP for Lynch syndrome: an updated third edition of the Mallorca guidelines based on gene and gender. 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
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR