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): disrupts the canonical splice-acceptor AG dinucleotide, predicting exon 16 skipping that shifts the reading frame and triggers nonsense-mediated decay.

2

PM2 (Supporting): variant is absent from gnomAD v4.1.

3

PP5 (Supporting): InSiGHT expert panel classifies the exact variant as Likely pathogenic (ClinVar 3-star).

4

Overall: Pathogenic, per Rule 4 (1 Very Strong + 2 Supporting) of the InSiGHT/ClinGen MLH1 VCEP v2.0 framework.

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

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 AG dinucleotide, predicting exon 16 skipping that shifts the reading frame and triggers nonsense-mediated decay. Flagged for human review: the reported SpliceAI max delta of 0.00 conflicts with expected biology and appears to be a tool artifact.	cspec pvs1_gene_context pvs1_variant_assessment spliceai
PS1	N/A	Not applicable: this splice-site variant produces no amino acid substitution, so the same-amino-acid-change rule cannot apply.	cspec
PS2	Not assessed	Not assessed: no parental testing or other evidence establishes that the variant arose de novo.	cspec
PS3	Not assessed	Not assessed: no functional assay of this exact variant is available; a minigene study tested the related c.1732-2A>T change, not this A>G allele.
PS4	N/A	Not applicable: the MLH1 expert panel specification does not use this criterion.	cspec
PM1	N/A	Not applicable: the MLH1 expert panel specification designates PM1 as not applicable, with no hotspot rule defined.	cspec
PM2	Met	Met (Supporting): absent from gnomAD v4.1, below the required allele-frequency threshold of 0.00002.	cspec gnomad_v4
PM3	Not assessed	Not assessed: no second MLH1 variant, phase information, or CMMRD clinical evidence was available to apply the co-occurrence rule.	cspec gnomad_v4
PM4	N/A	Not applicable: the MLH1 specification does not use PM4, and this splice-site change is not an in-frame indel.	cspec
PM5	N/A	Not applicable: no amino acid substitution exists to compare, so the different-missense-at-same-residue rule cannot apply.	cspec
PM6	N/A	Not applicable: the MLH1 specification routes de novo evidence to PS2 and does not use PM6.	cspec
PP1	Not assessed	Not assessed: only an unverified statement of familial segregation was available, with no pedigree or informative meioses to quantify.	clinvar cspec
PP2	N/A	Not applicable: the MLH1 expert panel specification designates PP2 as not applicable for this gene.	cspec
PP3	N/A	Not applicable: the variant sits at the canonical -2 acceptor position, which the specification routes to PVS1 rather than SpliceAI-based PP3.	cspec
PP4	Not assessed	Not assessed: tumor findings were reported, but without a primary source or confirmation that MLH1 promoter methylation was excluded.	cspec clinvar
PP5	Met	Met (Supporting): the InSiGHT expert panel classified this exact variant as Likely pathogenic (ClinVar 3-star).	clinvar
BA1	Not met	Not met: BA1 requires allele frequency >=0.001, but the variant is absent from gnomAD v4.1.	cspec gnomad_v4
BS1	Not met	Not met: BS1 requires allele frequency 0.0001-0.001, but the variant is absent from gnomAD v4.1.	cspec gnomad_v4
BS2	Not assessed	Not assessed: no confirmed in-trans co-occurrence with a pathogenic MLH1 variant was available.	cspec
BS3	Not assessed	Not assessed: no functional assay demonstrates normal splicing or protein function; the benign no-aberration rule does not apply to canonical splice sites.
BS4	Not assessed	Not assessed: no affected relative tested negative for the variant, so no non-segregation evidence exists.	cspec
BP1	N/A	Not applicable: the MLH1 expert panel specification designates BP1 as not applicable for this gene.	cspec
BP2	N/A	Not applicable: the MLH1 specification designates BP2 as not applicable.	cspec
BP3	N/A	Not applicable: the MLH1 specification does not use BP3, and this splice-site substitution is not an in-frame repeat-region indel.	cspec
BP4	N/A	Not applicable: the canonical acceptor position is evaluated under PVS1, and a splicing-neutral call would contradict the near-certain disruption of the obligate AG acceptor.	cspec spliceai
BP5	Not assessed	Not assessed: insufficient evidence on tumor phenotype, MMR loss, or BRAF/methylation status to apply the inconsistency rule.	cspec clinvar
BP6	Not met	Not met: the expert-panel classification is Likely pathogenic, not benign, so no benign assertion supports BP6.	clinvar
BP7	N/A	Not applicable: at intronic position -2, the variant sits inside the canonical splice region, not in the -21/+7 zone BP7 covers.	cspec

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