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MLH1
Final classification
Uncertain Significance - Conflicting Evidence
MLH1 c.1344G>T · p.Glu448Asp
MLH1

NM_000249.4:c.1344G>T (p.Glu448Asp) is a missense variant in exon 12 of the MLH1 gene. It is extremely rare in population databases, with an allele frequency of 1.92e-05 in gnomAD v4.1 (31/1,614,034 alleles, 0 homozygotes), meeting PM2 at supporting strength.

Gene
MLH1
Transcript
NM_000249.4
HGVS · transcript:coding
NM_000249.4:c.1344G>T
Consequence
N/A
GRCh38
chr3:37025942 G>T
GRCh37
chr3:37067433 G>T
Basis ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MLH1 Version 2.0 v2.0 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 v2.0 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.1344G>T

NM_000249.4:c.1344G>T (p.Glu448Asp) is a missense variant in exon 12 of the MLH1 gene. It is extremely rare in population databases, with an allele frequency of 1.92e-05 in gnomAD v4.1 (31/1,614,034 alleles, 0 homozygotes), meeting PM2 at supporting strength.1 Computational evidence strongly predicts a benign effect: the HCI prior probability for pathogenicity is 0.0024 (BP4_Supporting threshold <0.11 met), BayesDel score is -0.059 (benign range), and SpliceAI predicts no splicing impact (max delta = 0.03).2 No functional data are available for this variant. It is not included in the VCEP calibrated functional assay documentation, and no publication reports variant-specific functional evidence for c.1344G>T.3 No segregation, de novo, or tumor pathology data are available for this variant. The variant has been reported in ClinVar as Uncertain Significance (VariationID 127612, 1-star review status) by 14 clinical laboratories, with one additional submission as Benign and one as Likely Benign.4 Applying the InSiGHT VCEP v2.0 combination rules: one pathogenic supporting criterion (PM2_Supporting) and one benign supporting criterion (BP4_Supporting) are met. No criteria at moderate, strong, or very strong strength are met in either direction. This yields a classification of Uncertain Significance.5

PM2 + BP4 Uncertain Significance - Conflicting Evidence
Gene diagram · NM_000249.4 · variants mapped to exon structure
MLH1 NM_000249.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 15 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
The variant is extremely rare in population databases. In gnomAD v4.1, the overall allele frequency is 1.92e-05 (31/1,614,034 alleles, 0 homozygotes), which is below the VCEP PM2 threshold of <0.00002 (<1 in 50,000 alleles). The variant is absent from gnomAD-Canada v1.0.
gnomAD v4.1 AF = 1.92e-05 (31/1614034 alleles
BP4 supporting Benign
The HCI prior probability for pathogenicity is 0.0024, which is below the VCEP BP4_Supporting threshold of <0.11. Multiple in silico tools predict a benign effect: BayesDel score is -0.059 (benign range) and SpliceAI predicts no splicing impact (max delta = 0.03). REVEL score of 0.537 is indeterminate and does not override the HCI prior.
HCI prior = 0.0024 (BP4 threshold <0.11 met)BayesDel = -0.059SpliceAI max delta = 0.03
Assessed · not applied
Pathogenic
PVS1 NM_000249.4:c.1344G>T is a missense variant (p.Glu448Asp) in exon 12 of MLH1.
PS1 No other nucleotide change encoding p.Glu448Asp has been established as Pathogenic by this VCEP.
PS2 No de novo occurrence data are available for this variant.
PS3 No calibrated functional assay data exist for NM_000249.4:c.1344G>T (p.Glu448Asp).
PM5 No different missense change at codon 448 has been classified as Pathogenic or Likely Pathogenic by the InSiGHT VCEP.
PP1 No co-segregation data are available for this variant.
PP3 The HCI prior probability for pathogenicity is 0.0024, which is far below the VCEP PP3_Supporting threshold of >0.68.
PP4 No tumor data (MSI status, immunohistochemistry for MMR proteins) are available for patients carrying this variant.
Benign
BA1 The gnomAD v4.1 grpmax filtering allele frequency is 5.798e-05 (0.0058%), which is far below the VCEP BA1 threshold of >=0.001 (0.1%).
BS1 The gnomAD v4.1 grpmax filtering allele frequency is 5.798e-05 (0.0058%), which is below the VCEP BS1 threshold of >=0.0001 to <0.001.
BS2 No data are available for co-occurrence in trans with a known pathogenic MLH1 variant in a patient with CRC after age 45 without CMMRD features.
BS3 No functional data demonstrating a benign effect are available for this variant.
BS4 No segregation data are available to assess lack of co-segregation with disease.
BP5 No tumor data are available to demonstrate microsatellite stability (MSS) or intact MMR protein expression in CRC/endometrial tumors from patients carrying this variant.
BP7 BP7 applies to synonymous (silent) or intronic variants at or beyond -21/+7 splice positions.
N/A · 11 PS4 · PM1 · PM3 · PM4 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP6
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= 1.92065e-05; MAF= 0.00192%, 31/1614034 alleles, homozygotes = 0) and has highest observed frequency in the Middle Eastern population (AF= 0.000328731; MAF= 0.03287%, 2/6084 alleles, homozygotes = 0); grpmax FAF= 5.798e-05.
v2.1
This variant is present in gnomAD v2.1 (AF= 1.59242e-05; MAF= 0.00159%, 4/251190 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.000163239; MAF= 0.01632%, 1/6126 alleles, homozygotes = 0); grpmax FAF= 9.58e-06.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0019% · 31 / 1,614,034
0 hom · FAF 0.0058%
Middle Eastern
2 / 6,084
0.033%
Admixed American
3 / 59,986
0.005%
Remaining individuals
2 / 62,486
0.0032%
European (non-Finnish)
24 / 1,180,042
0.002%
+ 6 not observed (European (Finnish), Amish, East Asian, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0016% · 4 / 251,190
0 hom · FAF 0.00096%
Remaining individuals
1 / 6,126
0.016%
Admixed American
2 / 34,586
0.0058%
European (non-Finnish)
1 / 113,602
0.00088%
+ 5 not observed (African/African American, Ashkenazi Jewish, East Asian, European (Finnish), 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 (11 clinical laboratories) and as Uncertain Significance (1 clinical laboratory) and as Benign (1 clinical laboratory) and as Likely benign (1 clinical laboratory). (ClinVarID = 127612)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.537. BayesDel score = -0.0591115. HCI prior probability for pathogenicity = 0.0024. Custom PP2 score = 0.002.
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 ↗
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot.
Hotspots
This variant does not lie in a statistically significant hotspot.
Hotspots ↗
Sources & reference links
8Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
Cancer hotspots
Triaged references · 9 PMIDs not cited in assessment
15662714 ↗ Identification of Muir-Torre syndrome among patients with sebaceous tumors and keratoacanthomas: role of clinical features, microsatellite instability, and immunohistochemistry. 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
20301390 ↗ Lynch Syndrome. 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
25452455 ↗ Hereditary colorectal cancer syndromes: American Society of Clinical Oncology Clinical Practice Guideline endorsement of the familial risk-colorectal cancer: European Society for Medical Oncology Clinical Practice Guidelines. CLINVAR
25559809 ↗ Genetic diagnosis of high-penetrance susceptibility for colorectal cancer (CRC) is achievable for a high proportion of familial CRC by exome sequencing. CLINVAR
26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Versi CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR