Classification rationale

BP4 VUS

MLH1 c.1039-6dup

BP4 (Supporting): intronic variant with SpliceAI max delta 0.01, predicting no splicing impact (at or below the 0.1 threshold). No other criterion is met or applied, and a single BP4 (Supporting) satisfies no VCEP combination rule for Likely Benign (which requires one Benign.Strong plus one Benign.Supporting, or two Benign.Supporting); the variant is therefore classified as Variant of Uncertain Significance.

BP4 → VUS

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

MLH1 NM_000249.4

Fetching transcript structure from UCSC…

Applied criteria · 1 applied · 16 assessed

Applied · 1

Strength Supporting Moderate Strong Very strong

✓

BP4 supporting Benign

Met (Supporting): SpliceAI predicts no splicing impact (max delta 0.01, below the 0.1 threshold).

SpliceAI lookup (spliceai): max delta score = 0.01 (DS_AG 0.0, DS_AL 0.01, DS_DG 0.0, DS_DL 0.01) - delta <= 0.1, i.e. no predicted splicing impact.InSiGHT MMR VCEP MLH1 v2.0 BP4 rule (cspec): 'For intronic and synonymous variants: SpliceAI predicts no splicing impact with delta score <= 0.1 as per Walker et al 2023' - named threshold publication: Walker LC et al., Am J Hum Genet 2023;110(7):1046-1067, PMID 37352859 (as cited in the VCEP rule text and the cspec reference list).

spliceai ↗cspec ↗

Assessed · not applied

Pathogenic

PVS1 Not met: this intronic duplication is not a null variant, and SpliceAI predicts no splicing impact (max delta 0.01).

PS1 Not met: the variant produces no amino acid change (p.?) and no pathogenic variant at the same nucleotide exists.

PS2 Not assessed: no proband phenotype or parental-testing data exists to establish a de novo event.

PS3 Not assessed: no variant-specific functional, mRNA, or monoallelic expression assay data was available.

PM2 Not assessed: insufficient population-frequency evidence was available to apply PM2.

PM3 Not met: no biallelic CMMRD co-occurrence evidence exists, and gnomAD AF 0.053% far exceeds the <0.002% precondition.

PP1 Not assessed: no pedigree or segregation data exists to compute a co-segregation likelihood ratio.

PP3 Not met: SpliceAI max delta 0.01 is far below the 0.2 PP3 splice-threshold.

PP4 Not assessed: no variant-specific tumor data (MSI, MMR immunohistochemistry, or methylation) was available.

Benign

BA1 Not assessed: insufficient population-frequency evidence was available to apply BA1.

BS1 Not assessed: insufficient population-frequency evidence was available to apply BS1.

BS2 Not assessed: insufficient population-frequency evidence was available to apply BS2.

BS3 Not assessed: no variant-specific mRNA or functional laboratory assay data was available to demonstrate proficient function.

BS4 Not assessed: no family segregation data exists; absence of data cannot demonstrate lack of co-segregation.

BP5 Not assessed: no variant-specific tumor data (MSS status, MMR immunohistochemistry, BRAF, methylation) was available.

BP7 Not met: the variant lies at position -6, inside the splice-relevant window, not at or beyond -21 as BP7 requires.

N/A · 11 PS4 · PM1 · PM4 · PM5 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP6

Research & evidence

Population frequency

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

22855150 ↗ Guidelines for biomarker testing in colorectal carcinoma (CRC): a national consensus of the Spanish Society of Pathology (SEAP) and the Spanish Society of Medical Oncology (SEOM). CLINVAR

23012255 ↗ ESMO Consensus Guidelines for management of patients with colon and rectal cancer. a personalized approach to clinical decision making. 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

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

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