Variant classification summary

NM_000249.4:c.1732-2A>G

MLH1 · NP_000240.1:p.? · NM_000249.4

GRCh37: chr3:37089008 A>G · GRCh38: chr3:37047517 A>G

Gene: MLH1 Transcript: NM_000249.4

Final call

Pathogenic

PVS1 very strong PM2 supporting PP5 supporting

Variant details

Gene

MLH1

Transcript

NM_000249.4

Protein

NP_000240.1:p.?

gnomAD AF

ClinVar

Likely pathogenic

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

PVS1 (Very Strong): disruption of the canonical splice-acceptor -2 position is predicted to abolish the natural acceptor (SpliceAI max delta 0.996), with exon skipping expected to trigger nonsense-mediated decay.

2

PM2 (Supporting): absent from gnomAD v4.1, below the 0.00002 allele-frequency threshold.

3

PP5 (Supporting): the InSiGHT expert panel classified this variant as Likely pathogenic.

4

Synthesis: PVS1 (Very Strong) with PM2 and PP5 (Supporting) satisfies MLH1 InSiGHT VCEP Rule4 (1 Very Strong + at least 2 Supporting), producing a final classification of Pathogenic.

Final determination: Rule4 of the InSiGHT MLH1 VCEP v2.0 criteria-combination framework (1 Pathogenic.Very Strong + >=2 Pathogenic.Supporting) is satisfied by PVS1 (Very Strong) plus PM2 and PP5 (both Supporting), yielding Pathogenic.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Met	Met (Very Strong): disrupts the canonical splice-acceptor -2 position; SpliceAI predicts near-total acceptor loss (max delta 0.996), with exon skipping predicted to trigger nonsense-mediated decay. Caveat for review: the frameshift/NMD outcome was assumed, as RNA confirmation was not available.	cspec spliceai pvs1_gene_context pvs1_variant_assessment
PS1	N/A	Not applicable: this is a canonical splice-acceptor variant with no amino-acid change, outside both PS1 branches (missense or non-canonical splice nucleotide).	cspec
PS2	Not assessed	Not assessed: no de novo observation or parental test results were available.	cspec
PS3	Not assessed	Not assessed: no calibrated functional assay or RNA/cDNA study of this exact variant was available.
PS4	N/A	Not applicable: the MLH1 VCEP evaluates tumor immunohistochemistry through PP4 instead of PS4.	cspec
PM1	N/A	Not applicable: the MLH1 VCEP defines no mutational-hotspot PM1 rule for this gene.	cspec
PM2	Met	Met (Supporting): absent from gnomAD v4.1, below the 0.00002 allele-frequency threshold.	cspec gnomad_v4
PM3	Not assessed	Not assessed: no evidence of a second MLH1 variant or phase information indicating CMMRD was available.	cspec gnomad_v4
PM4	N/A	Not applicable: the MLH1 VCEP does not use PM4, and this splice variant has no defined protein length change.	cspec
PM5	N/A	Not applicable: no amino-acid substitution results (p.?), so there is no residue to compare against other missense changes.	pm5_candidates
PM6	N/A	Not applicable: the MLH1 VCEP does not use PM6; unconfirmed de novo observations are handled through PS2.	cspec
PP1	Not assessed	Not assessed: no pedigree genotypes or segregation data were available.	cspec
PP2	N/A	Not applicable: the MLH1 VCEP does not use PP2, and this is not a missense variant.	cspec
PP3	N/A	Not applicable: PP3 is restricted to non-canonical splice sites and missense variants; canonical splice disruption is scored under PVS1 without double-counting the same splice evidence.	cspec spliceai
PP4	Not assessed	Not assessed: an MSI-H tumor with MLH1/PMS2 loss was reported, but no primary tumor report confirmed the MSI method, tumor independence, or methylation exclusion.	cspec clinvar
PP5	Met	Met (Supporting): the InSiGHT expert panel classified this variant as Likely pathogenic.	clinvar
BA1	Not met	Not met: absent from gnomAD v4.1, so the BA1 population-frequency threshold cannot be reached.	cspec gnomad_v4
BS1	Not met	Not met: absent from gnomAD v4.1, so the BS1 population-frequency range cannot be reached.	cspec gnomad_v4
BS2	Not assessed	Not assessed: no confirmed in-trans occurrence with a known pathogenic MLH1 variant was documented.	cspec
BS3	Not assessed	Not assessed: no calibrated functional assay demonstrated normal or proficient MLH1 function for this variant.
BS4	Not assessed	Not assessed: no non-segregation observations or pedigree likelihood data were available.	cspec
BP1	N/A	Not applicable: the MLH1 VCEP does not use BP1, and this is a splice variant, not a missense change.	cspec
BP2	N/A	Not applicable: the MLH1 VCEP does not use BP2, directing use of BS2 instead.	cspec
BP3	N/A	Not applicable: the MLH1 VCEP does not use BP3, and this is not an in-frame deletion/insertion.	cspec
BP4	N/A	Not applicable: BP4 covers missense or non-canonical splice variants with SpliceAI delta <=0.1; this canonical splice variant scores 0.996.	cspec spliceai
BP5	Not assessed	Not assessed: no evidence of an alternative molecular basis, such as MLH1 promoter methylation or BRAF V600E-positive tumors, was available.	cspec
BP6	Not assessed	Not assessed: no expert-panel benign classification exists; the only panel assertion is InSiGHT Likely pathogenic.	clinvar
BP7	N/A	Not applicable: BP7 covers synonymous or deep-intronic variants at or beyond -21/+7, not a canonical -2 splice position.	cspec

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