Classification rationale

PM2 BP4 Uncertain Significance - Conflicting Evidence

MLH1 c.1637A>G

HCI prior probability for pathogenicity is 0.0023, meeting BP4_Supporting per InSiGHT VCEP v2.0.0 (threshold <0.11). REVEL (0.469) and BayesDel (-0.0407) are consistent with a benign in silico profile.¹ Extremely rare in gnomAD v4.1 (grpmax FAF = 1.24e-06; 6/1,613,836 alleles, 0 homozygotes), meeting PM2_Supporting per InSiGHT VCEP v2.0.0 (threshold <0.00002). Absent from gnomAD-Canada v1.0.² This variant has been reported in ClinVar (Variation ID: 127617) with submissions of Uncertain Significance (10 clinical laboratories), Benign (1), and Likely Benign (1); no expert panel classification is available.³ NM_000249.4:c.1637A>G (p.Lys546Arg) was observed in 1 of 711 patients with hereditary breast cancer in a Russian case-control study (PMID:32547938); no variant-specific MSI, IHC, or functional data were reported.⁴

PM2 + BP4 → Uncertain Significance - Conflicting Evidence

1 hci_priorrevelbayesdel

2 gnomad_v4 ↗gnomad_canada ↗

3 clinvar ↗

4 PMID:32547938 ↗

Gene diagram · NM_000249.4 · variants mapped to exon structure

MLH1 NM_000249.4

Fetching transcript structure from UCSC…

Applied criteria · 2 applied · 13 assessed

Applied · 2

Strength Supporting Moderate Strong Very strong

✓

PM2 supporting Pathogenic

Extremely rare in gnomAD v4.1: grpmax filtering allele frequency = 1.24e-06, which is below the VCEP PM2_Supporting threshold of <0.00002 (<1 in 50,000 alleles). Observed in 6/1,613,836 alleles (0 heterozygotes), with highest subpopulation frequency in African/African American (AF = 1.34e-05). Absent from gnomAD-Canada v1.0.

gnomAD v4.1 grpmax FAF = 1.24e-06

gnomad_v4 ↗

✓

BP4 supporting Benign

HCI prior probability for pathogenicity = 0.0023, which is below the VCEP BP4_Supporting threshold of <0.11. Multiple in silico predictors support a benign effect: REVEL = 0.469 (not predictive of pathogenicity), BayesDel = -0.0407 (slightly benign-leaning).

HCI prior probability = 0.0023 (<0.11 threshold)REVEL score = 0.469BayesDel score = -0.0407

Assessed · not applied

Pathogenic

PS1 No different underlying nucleotide change encoding the same amino acid substitution (Lys546Arg) has been established as Pathogenic or Likely Pathogenic by the InSiGHT VCEP.

PS2 No de novo observation reported in any reviewed literature.

PS3 This variant is not listed in the VCEP calibrated functional assay documentation (Functional-assay-SVI-documentation-MMR.xlsx) and no variant-specific functional data demonstrating a damaging effect on MMR function were identified in any reviewed publication.

PM5 No different missense variant at amino acid residue Lys546 has been classified as Pathogenic or Likely Pathogenic by the InSiGHT VCEP.

PP1 No co-segregation data available for this variant in any reviewed publication.

PP3 HCI prior probability for pathogenicity = 0.0023, well below the VCEP PP3_Supporting threshold of >0.68.

PP4 No MSI-H tumor data or MMR protein IHC loss data reported for this specific variant in any reviewed publication.

Benign

BA1 gnomAD v4 grpmax filtering allele frequency = 1.24e-06, far below the VCEP BA1 threshold of ≥0.001 (0.1%).

BS1 gnomAD v4 grpmax filtering allele frequency = 1.24e-06, below the VCEP BS1 threshold of ≥0.0001 (0.01%).

BS2 No evidence of co-occurrence in trans with a known pathogenic MLH1 variant in a patient meeting the specified clinical criteria (CRC after age 45 or other LS cancer above median onset age, without CMMRD features).

BS3 This variant is not listed in the VCEP calibrated functional assay documentation and no variant-specific functional data demonstrating proficient MMR function were identified in any reviewed publication.

BS4 No co-segregation analysis data available for this variant.

BP5 No tumor data demonstrating MSS status, lack of MMR protein loss, BRAF V600E mutation, or MLH1 promoter methylation were reported for this variant in any reviewed publication.

N/A · 11 PVS1 · PS4 · PM1 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP6 · BP7

Research & evidence

Population frequency

gnomAD v4.1

gnomAD v2.1

v4.1

This variant is present in gnomAD v4.1 (AF= 3.71785e-06; MAF= 0.00037%, 6/1613836 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 1.33529e-05; MAF= 0.00134%, 1/74890 alleles, homozygotes = 0); grpmax FAF= 1.24e-06.

v2.1

This variant is present in gnomAD v2.1 (AF= 7.95805e-06; MAF= 0.00080%, 2/251318 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.75982e-05; MAF= 0.00176%, 2/113648 alleles, homozygotes = 0); grpmax FAF= 2.92e-06.

🇨🇦 CA

Absent from gnomAD-Canada v1.0.

Allele frequency by ancestry

three datasets · side by side

gnomAD v4.1

0.00037% · 6 / 1,613,836
0 hom · FAF 0.00012%

African/African American 1 / 74,890	0.0013%
European (non-Finnish) 5 / 1,179,892	0.00042%

+ 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)

gnomAD v2.1

0.0008% · 2 / 251,318
0 hom · FAF 0.00029%

European (non-Finnish)

2 / 113,648

0.0018%

+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)

gnomAD Canada 🇨🇦

Absent · 0 / ?
0 hom

Not observed in any ancestry group.

gnomAD v4 ↗ gnomAD v2 ↗ gnomAD 🇨🇦 ↗

ClinVar

This variant has been reported in ClinVar as Uncertain significance (9 clinical laboratories) and as Uncertain Significance (1 clinical laboratory) and as Benign (1 clinical laboratory) and as Likely benign (1 clinical laboratory). (ClinVarID = 127617)

ClinVar ↗

In silico

SpliceAI predicts possible splice impact for this variant (max delta score = 0.36). REVEL score = 0.469. BayesDel score = -0.0406917. HCI prior probability for pathogenicity = 0.0023. MAPP score = 3.83. Custom PP2 score = 0.016.

SpliceAI ↗

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

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.

COSMIC ↗ Hotspots ↗

Sources & reference links

9Sources

CSpec VCEP

ClinVar

gnomAD v2.1

gnomAD v4.1

gnomAD-Canada

SpliceAI

OncoKB

COSMIC

Cancer hotspots

Triaged references · 9 PMIDs not cited in assessment

25070057 ↗ Guidelines on genetic evaluation and management of Lynch syndrome: a consensus statement by the US Multi-society Task Force on colorectal cancer. CLINVAR

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

26467025 ↗ A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders. CLINVAR

32547938 ↗ Lynch Syndrome Germline Mutations in Breast Cancer: Next Generation Sequencing Case-Control Study of 1,263 Participants. CLINVAR

32832836 ↗ Pathogenic Variants in Cancer Predisposition Genes and Prostate Cancer Risk in Men of African Ancestry. CLINVAR

23408351 ↗ Revised guidelines for the clinical management of Lynch syndrome (HNPCC): recommendations by a group of European experts. CLINVAR

23535968 ↗ Informing family members of individuals with Lynch syndrome: a guideline for clinical geneticists. CLINVAR

24310308 ↗ ACMG technical standards and guidelines for genetic testing for inherited colorectal cancer (Lynch syndrome, familial adenomatous polyposis, and MYH-associated polyposis). CLINVAR

28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR

Re-run this variant?