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MLH1
Final classification
VUS
MLH1 c.342_347del · p.Ile115_Thr116del
MLH1

NM_000249.4:c.342_347del (p.Ile115_Thr116del) is an in-frame deletion in exon 4 of MLH1. It is absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada), meeting PM2_Supporting under the InSiGHT MLH1 VCEP framework.

Gene
MLH1
Transcript
NM_000249.4
HGVS · transcript:coding
NM_000249.4:c.342_347del
Consequence
N/A
GRCh38
chr3:37004431 GTTACTA>G
GRCh37
chr3:37045922 GTTACTA>G
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 was evaluated deterministically with applied criteria: PM2 supporting; no rule matched the adjudicated criteria.
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 was evaluated deterministically with applied criteria: PM2 supporting; no rule matched the adjudicated criteria.
Classification rationale
PM2 VUS
MLH1 c.342_347del

NM_000249.4:c.342_347del (p.Ile115_Thr116del) is an in-frame deletion in exon 4 of MLH1. It is absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada), meeting PM2_Supporting under the InSiGHT MLH1 VCEP framework.1 Under the InSiGHT MLH1 VCEP v2.0.0, PVS1 is not applicable because this in-frame deletion does not introduce a premature termination codon and does not meet the VCEP criteria for nonsense, frameshift, or canonical splice variants.2 No functional studies, tumor phenotype data, segregation data, or de novo observations were identified for this variant in any reviewed publication or database. Six papers were reviewed in full text; none mention NM_000249.4:c.342_347del.3 This variant has been reported in ClinVar as Uncertain Significance (1 clinical laboratory, criteria provided, single submitter). Under the InSiGHT MLH1 VCEP framework, PP5 is not applicable and this single submission does not constitute independent evidence for classification.4 With PM2_Supporting as the only met criterion and no benign criteria met, this variant remains a Variant of Uncertain Significance under the InSiGHT MLH1 VCEP classification rules. All other applicable criteria are either not met, not applicable by VCEP designation, or cannot be assessed due to absence of data.5

PM2 VUS
Gene diagram · NM_000249.4 · variants mapped to exon structure
MLH1 NM_000249.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 11 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_000249.4:c.342_347del is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada, meeting the InSiGHT MLH1 VCEP PM2_Supporting threshold (allele frequency <0.00002 in gnomAD v4).
Absent from gnomAD v2.1 (0 alleles)Absent from gnomAD v4.1 (0 alleles)Absent from gnomAD-Canada v1.0 (0 alleles)
Assessed · not applied
Pathogenic
PVS1 NM_000249.4:c.342_347del is an in-frame deletion of 6 nucleotides removing Ile115 and Thr116 (p.Ile115_Thr116del).
PS2 No de novo observation data have been reported for NM_000249.4:c.342_347del in the available evidence.
PS3 No variant-specific functional studies or calibrated functional assay data were identified for NM_000249.4:c.342_347del in the literature or InSiGHT VCEP functional assay documentation.
PP1 No co-segregation data are available for NM_000249.4:c.342_347del in any reported pedigrees.
PP4 No tumor MSI or MMR immunohistochemistry data have been reported for patients carrying NM_000249.4:c.342_347del.
Benign
BA1 NM_000249.4:c.342_347del is absent from gnomAD v4.1; the InSiGHT MLH1 VCEP BA1 threshold requires a gnomAD v4 Grpmax filtering allele frequency >= 0.001 (0.1%), which is not met.
BS1 NM_000249.4:c.342_347del is absent from gnomAD v4.1; the InSiGHT MLH1 VCEP BS1 threshold requires a gnomAD v4 Grpmax filtering allele frequency >= 0.0001 (0.01%), which is not met.
BS2 No data are available regarding co-occurrence in trans with a known pathogenic MLH1 variant in a patient with colorectal or Lynch syndrome spectrum cancer after age 45 without CMMRD features.
BS3 No variant-specific functional studies demonstrating normal MMR function have been identified for NM_000249.4:c.342_347del in the literature or InSiGHT VCEP calibrated functional assay documentation.
BS4 No segregation data are available to evaluate lack of co-segregation with disease for NM_000249.4:c.342_347del.
BP5 No tumor phenotype data (MSS status, MMR IHC, BRAF V600E, or MLH1 promoter methylation) are available for patients carrying NM_000249.4:c.342_347del.
N/A · 15 PS1 · PS4 · PM1 · PM4 · PM5 · PM6 · PP2 · PP3 · PP5 · BP1 · BP2 · BP3 · BP4 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
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
Not observed in any ancestry group.
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 (1 clinical laboratory). (ClinVarID = 4081840)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
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
22138009 ↗ NCCN Task Force report: Evaluating the clinical utility of tumor markers in oncology. CLINVAR
23852704 ↗ Tumor markers in colorectal cancer, gastric cancer and gastrointestinal stromal cancers: European group on tumor markers 2014 guidelines update. 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
20301390 ↗ Lynch Syndrome. CLINVAR
25373533 ↗ Updated guidelines for biomarker testing in colorectal carcinoma: a national consensus of the Spanish Society of Pathology and the Spanish Society of Medical Oncology. CLINVAR
32418154 ↗ Update of the recommendations for the determination of biomarkers in colorectal carcinoma: National Consensus of the Spanish Society of Medical Oncology and the Spanish Society of Pathology. CLINVAR