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NM_000249.4:c.1039-6dup
p.? · MLH1
ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MLH1 Version 2.0 · v2.0
0%
complete
Final classification
Benign
BA1BP4
MLH1
c.1039-6dup
p.?
Gene context NCBI Gene ↗ OncoKB ↗

MLH1 encodes a DNA mismatch repair protein that, together with partners such as PMS2, corrects errors that arise during DNA replication. Loss of this repair function leads to the accumulation of mutations, particularly in repetitive microsatellite sequences, and tumors with defective MLH1 typically show high microsatellite instability. Germline mutations in MLH1 cause Lynch syndrome (hereditary non-polyposis colorectal cancer), which strongly predisposes to colorectal, endometrial, ovarian, and other cancers, while biallelic mutations cause constitutional mismatch repair deficiency (CMMRD). Because it normally protects against cancer by maintaining genomic stability, MLH1 acts as a tumor suppressor, and mismatch-repair-deficient tumors often respond well to immunotherapy.

This variant

MLH1 corrects DNA replication errors through mismatch repair, and germline loss of this function causes Lynch syndrome with high microsatellite instability tumors. This intronic variant, present at 0.05% allele frequency in gnomAD v4.1 and predicted to have no splicing impact, is not expected to impair MLH1's repair function; the Benign classification means it does not confer Lynch syndrome risk.

Transcript
NM_000249.4
HGVS · transcript:coding
NM_000249.4:c.1039-6dup
GRCh38
chr3:37025629 T>TA
GRCh37
chr3:37067120 T>TA
Benign under ClinGen InSiGHT MLH1 VCEP v2.0 (Rule17, Benign Stand-Alone): BA1 met with gnomAD v4.1 grpmax FAF 0.00117 >= 0.001, plus BP4 supporting (SpliceAI max delta 0.01); no pathogenic criterion met.
Classification rationale
BA1BP4 Benign
MLH1 c.1039-6dup

BA1 (stand-alone benign): gnomAD v4.1 grpmax FAF 0.00117 exceeds the 0.001 threshold, and the variant is excluded as a founder pathogenic variant. BP4 (Supporting): intronic variant with SpliceAI max delta 0.01 (<=0.1), predicting no splicing impact. Final classification: Benign, per InSiGHT MLH1 VCEP v2.0 Rule17 (Benign Stand-Alone via BA1).

BA1 + BP4 → Benign
LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
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
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
BA1 stand-alone Benign
Met: gnomAD v4.1 grpmax FAF 0.00117 exceeds the >=0.001 stand-alone threshold, and the variant is excluded as a founder pathogenic variant. Flagged for review: grpmax FAF 0.00117 sits close to the 0.001 threshold, and gnomAD raw data flagged a low-complexity dupA context.
gnomAD v4.1 joint grpmax FAF 0.00117106 (>= 0.001 threshold); total AF 0.000530357 (653/1,231,246 alleles); AFR AF 0.00142622 (78/54,690); 1 homozygote (ASJ)gnomAD v2.1 total AF 0.000263237 (37/140,558 alleles), grpmax FAF 0.00082842, 0 homozygotes (cross-version frequency consistency)ClinVar VCV000140797: Benign (5 clinical laboratories) and Likely benign (4 clinical laboratories), no expert panel submissions
gnomad_v4 ↗gnomad_v2 ↗gnomad_canada ↗clinvar ↗cspec ↗
BP4 supporting Benign
Met: intronic variant with SpliceAI max delta 0.01, at or below the <=0.1 no-splicing-impact threshold, meeting BP4 supporting.
SpliceAI Lookup (source_registry key 'spliceai'): max delta score 0.01 (DS_AG 0.0, DS_AL 0.01, DS_DG 0.0, DS_DL 0.01) for NM_000249.4:c.1039-6dup.InSiGHT MLH1 VCEP v2.0 BP4 rule (source_registry key 'cspec'; CSPEC doc 1564688410): 'For intronic and synonymous variants: SpliceAI predicts no splicing impact with delta score <= 0.1 as per Walker et al 2023.' Walker et al 2023 = PMID 37352859 (Am J Hum Genet 110(7):1046-1067, 2023), per cspec raw_rule_origin.references. Variant is intronic and SpliceAI max delta 0.01 <= 0.1 -> BP4_Supporting met.HCI prior BP4 path (<0.11 -> BP4_Supporting) is missense-only per HCI-PRIORS-MLH1.txt index guidance (source_registry key 'vcep_hci_priors_mlh1'); not applicable to this intronic variant.
spliceai ↗cspec ↗
Assessed · not applied · 7 not met · 8 not assessed
Pathogenic
PVS1 Not met: intronic variant with no predicted protein consequence and SpliceAI max delta 0.01, so no loss-of-function mechanism is established.
PS1 Not met: no pathogenic splice variant at the same nucleotide exists for comparison, and SpliceAI max delta 0.01 predicts no splicing impact.
PS2 Not assessed: no de novo observation or parental testing data was reported for this variant.
PS3 Not assessed: no variant-specific functional assay data was available - no calibrated assay odds, MMR function, or RNA expression results.
PM2 Not met: gnomAD v4.1 allele frequency 0.053% is more than 26-fold above the <0.002% PM2 rarity threshold.
PM3 Not met: no observation in trans with a pathogenic variant exists, and the 0.05% population frequency is far too high for a pathogenic Lynch syndrome allele.
PP1 Not assessed: no pedigree or segregation data was available to compute a co-segregation likelihood ratio.
PP3 Not met: SpliceAI max delta 0.01 is well below the >=0.2 splice-defect threshold, and missense scoring does not apply to this intronic variant.
PP4 Not assessed: no tumor phenotype data was available - no MSI status, MMR immunohistochemistry, or MLH1 promoter methylation results.
Benign
BS1 Not met: grpmax FAF 0.00117 falls above the 0.01-0.1% BS1 band, so the variant instead meets the BA1 stand-alone threshold.
BS2 Not assessed: no patient-level genotype data was available, including any in-trans co-occurrence with a pathogenic variant.
BS3 Not assessed: no RNA-based or calibrated functional assay data existed to demonstrate normal splicing or protein function.
BS4 Not assessed: no pedigrees were available to compute the required non-segregation likelihood ratio.
BP5 Not assessed: no tumor phenotype data was available - no MSS status, MMR immunohistochemistry, BRAF V600E, or MLH1 methylation results.
BP7 Not met: the variant sits at intronic position -6, inside the splice-region window, not at or beyond -21/+7 as BP7 requires.
N/A · 11 PS4 · PM1 · PM4 · PM5 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP6
Research & evidence
Population frequency · supports benign
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= 0.000530357; MAF= 0.05304%, 653/1231246 alleles, homozygotes = 1) and has highest observed frequency in the African/African American population (AF= 0.00142622; MAF= 0.14262%, 78/54690 alleles, homozygotes = 0); grpmax FAF= 0.00117106.
v2.1
This variant is present in gnomAD v2.1 (AF= 0.000263237; MAF= 0.02632%, 37/140558 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000807103; MAF= 0.08071%, 10/12390 alleles, homozygotes = 0); grpmax FAF= 0.00082842.
🇨🇦 CA
This variant is present in gnomAD-Canada v1.0 (AF= 0.0007809885083119491, 14/17926 alleles, homozygotes = 0).
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.053% · 653 / 1,231,246
1 hom · FAF 0.12%
African/African American
78 / 54,690
0.14%
Remaining individuals
24 / 45,318
0.053%
European (non-Finnish)
503 / 953,590
0.053%
Admixed American
13 / 31,092
0.042%
East Asian
12 / 33,916
0.035%
Middle Eastern
1 / 3,444
0.029%
Ashkenazi Jewish
6 / 20,848
0.029%
1 hom
European (Finnish)
10 / 44,710
0.022%
South Asian
6 / 42,746
0.014%
+ 1 not observed (Amish)
gnomAD v2.1
0.026% · 37 / 140,558
0 hom · FAF 0.083%
African/African American
10 / 12,390
0.081%
Ashkenazi Jewish
2 / 5,092
0.039%
Remaining individuals
1 / 2,970
0.034%
European (non-Finnish)
18 / 70,584
0.026%
South Asian
4 / 16,438
0.024%
European (Finnish)
2 / 15,848
0.013%
+ 2 not observed (Admixed American, East Asian)
gnomAD Canada 🇨🇦
0.078% · 14 / 17,926
0 hom · FAF 0.084%
⚠ LCR indel · split
Middle Eastern
1 / 140
0.71%
African/African American
3 / 978
0.31%
Remaining individuals
1 / 1,104
0.091%
South Asian
1 / 1,344
0.074%
European (non-Finnish)
8 / 11,384
0.07%
+ 4 not observed (Latino/Admixed American, Ashkenazi Jewish, East Asian, European (Finnish))
gnomAD v4 ↗ gnomAD v2 ↗ gnomAD 🇨🇦 ↗
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Benign (5 clinical laboratories) and as Likely benign (4 clinical laboratories). (ClinVarID = 140797)
ClinVar ↗
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
SpliceAI ↗
Functional No data
No calibrated functional assay or RNA evidence was identified for this variant.
OncoKB ↗
COSMIC screenshot
COSMIC
Somatic evidence
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant cancer hotspot.
COSMIC ↗
Sources & reference links
8Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Triaged references · 7 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
23429431 ↗ Recommendations from the EGAPP Working Group: can testing of tumor tissue for mutations in EGFR pathway downstream effector genes in patients with metastatic colorectal cancer improve health outcomes by guiding decisions regarding anti-EGFR therapy? 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
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
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
19042984 ↗ National Academy of Clinical Biochemistry laboratory medicine practice guidelines for use of tumor markers in testicular, prostate, colorectal, breast, and ovarian cancers. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR