PM2_supporting met: variant is absent from gnomAD v4.1, meeting the VCEP allele frequency threshold of <0.00002 (<1 in 50,000 alleles).1 BP4_supporting met: HCI prior probability for pathogenicity is 0.0146 (<0.11), consistent with a benign in silico prediction. REVEL score 0.604 and BayesDel 0.161 also favor a benign interpretation.2 PP3 not met: HCI prior 0.0146 does not reach the PP3 supporting threshold of >0.68. SpliceAI delta 0.00 does not indicate splicing impact.3 PS3 not met: no variant-specific functional data from calibrated MMR assays available. OncoKB reports Unknown Oncogenic Effect.4 PVS1 not applicable: this is a missense variant and does not meet any VCEP PVS1 rule criteria.5 Overall, one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4) are met, yielding insufficient evidence for classification. Defaults to Uncertain Significance per ACMG/AMP 2015 framework.6
MLH1
Final classification
Uncertain Significance - Conflicting Evidence
MLH1 c.1433A>G · p.Asp478Gly
MLH1
PM2_supporting met: variant is absent from gnomAD v4.1, meeting the VCEP allele frequency threshold of <0.00002 (<1 in 50,000 alleles).
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; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PM2
BP4
Uncertain Significance - Conflicting Evidence
MLH1 c.1433A>G
PM2 + BP4
→
Uncertain Significance - Conflicting Evidence
2
hci_priorrevelbayesdel
3
hci_priorspliceai ↗
4
oncokb ↗vcep_functional_assay_svi_documentation_mmr
5
pvs1_gene_contextpvs1_variant_assessment
6
cspec ↗
Gene diagram
· NM_000249.3 · variants mapped to exon structure
MLH1
NM_000249.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 13 assessed
Applied · 2
Strength
Supporting
Moderate
Strong
Very strong
✓
PM2
supporting
Pathogenic
This variant is absent from gnomAD v4.1, meeting the VCEP PM2_supporting threshold of allele frequency <0.00002 (<1 in 50,000 alleles). It is also absent from gnomAD v2.1 and gnomAD-Canada v1.0.
Absent from gnomAD v4.1 (AF <0.00002)Absent from gnomAD v2.1Absent from gnomAD-Canada v1.0
✓
BP4
supporting
Benign
The HCI prior probability for pathogenicity is 0.0146, which is <0.11, meeting the VCEP BP4_Supporting threshold for missense variants. Multiple in silico tools predict a benign impact: REVEL score 0.604 (below typical pathogenic threshold), BayesDel 0.161, and SpliceAI max delta 0.00 (no predicted splicing effect).
HCI prior probability: 0.0146 (threshold: <0.11 for BP4_Supporting)SpliceAI max delta: 0.00REVEL: 0.604
Assessed · not applied
Pathogenic
PS1
No different nucleotide change encoding the same amino acid substitution (p.Asp478Gly) has been classified as Pathogenic or Likely Pathogenic by the InSiGHT MMR VCEP.
PS2
No de novo observations reported for this variant.
PS3
No variant-specific functional data from calibrated MMR assays exists.
PM5
No pathogenic or likely pathogenic missense variant at the same amino acid residue (Asp478) has been classified by the InSiGHT MMR VCEP.
PP1
No co-segregation data available for this variant.
PP3
The HCI prior probability for pathogenicity is 0.0146, which does not meet the VCEP PP3 thresholds (>0.68 for supporting, >0.81 for moderate).
PP4
No tumor MSI or IHC data available.
Benign
BA1
This variant is absent from gnomAD v4.1, which does not meet the VCEP BA1 threshold of gnomAD v4 Grpmax filtering allele frequency ≥0.001 (0.1%).
BS1
This variant is absent from gnomAD v4.1, which does not meet the VCEP BS1 threshold of gnomAD v4 Grpmax filtering allele frequency ≥0.0001 and <0.001 (0.01-0.1%).
BS2
No data on co-occurrence in trans with a known pathogenic variant in the same gene in a CRC patient after age 45 without CMMRD features.
BS3
No functional data from calibrated MMR assays demonstrating proficient function exists for this variant.
BS4
No co-segregation data available.
BP5
No tumor phenotype data available.
N/A · 13
PVS1 · PS4 · PM1 · PM3 · PM4 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
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
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
ClinVar
This variant has been reported in ClinVar as Uncertain significance (2 clinical laboratories). (ClinVarID = 418302)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.604. BayesDel score = 0.160558. HCI prior probability for pathogenicity = 0.0146. MAPP score = 8.56. Custom PP2 score = 0.027.
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.
COSMIC
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
Triaged references · 1 PMID not cited in assessment
28492532 ↗
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
CLINVAR