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

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

✓

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

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

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

This variant has been reported in ClinVar as Benign (5 clinical laboratories) and as Likely benign (4 clinical laboratories). (ClinVarID = 140797)

ClinVar ↗

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

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