Variant classification summary

NM_000249.4:c.1558+4C>T

MLH1 · NP_000240.1:p.? · NM_000249.4

GRCh37: chr3:37070427 C>T · GRCh38: chr3:37028936 C>T

Gene: MLH1 Transcript: NM_000249.4

Final call

VUS

PM2 supporting BP4 supporting

Variant details

Gene

MLH1

Transcript

NM_000249.4

Protein

NP_000240.1:p.?

gnomAD AF

2.478385381491666e-06 (v4.1)

ClinVar

Uncertain significance

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

PM2 (Supporting): allele frequency 2.478e-06 in gnomAD v4.1 (4/1,613,954 alleles), below the <0.00002 threshold.

2

BP4 (Supporting): SpliceAI max delta 0.00 is at or below the <=0.1 threshold, predicting no splicing impact for this intronic variant.

3

Overall: VUS (Uncertain Significance - Conflicting Evidence), per Rule31 requiring at least one benign-supporting and one pathogenic-supporting criterion.

Final determination: Under the ClinGen InSiGHT MLH1 VCEP v2.0 criteria-combination framework, at least one Benign-supporting criterion (BP4) together with at least one Pathogenic-supporting criterion (PM2) satisfies Rule31, which infers 'Uncertain Significance - Conflicting Evidence' (VUS in the five-tier schema); no rule for Pathogenic, Likely Pathogenic, Benign, or Likely Benign is satisfied by the adjudicated criteria.

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	Not met	Not met: intronic +4 variant with no predicted protein consequence and SpliceAI max delta 0.00, so no loss-of-function mechanism is established.	cspec spliceai
PS1	Not met	Not met: no Pathogenic or Likely Pathogenic variant at the same +4 nucleotide exists, and SpliceAI max delta is 0.00.	cspec spliceai pm5_candidates clinvar
PS2	Not assessed	Not assessed: no parental testing or reported de novo occurrence is available to score de novo evidence.	cspec clinvar
PS3	Not assessed	Not assessed: no calibrated functional assay, MMR defect, or mRNA expression data exists for this variant.	cspec vcep_functional_assay_svi_documentation_mmr vcep_vcep_pilot_variants_mmr clinvar
PS4	N/A	Not applicable: the MLH1 VCEP does not use proband counting (PS4), and no case-control enrichment data exists for this variant.	cspec clinvar gnomad_v4 PMID:29887214
PM1	N/A	Not applicable: the MLH1 VCEP does not use PM1, and this intronic variant alters no amino acid residue.	cspec
PM2	Met	Met (Supporting): gnomAD v4.1 total allele frequency 2.478e-06 (4/1,613,954 alleles) is below the <0.00002 threshold.	gnomad_v4 gnomad_v2 gnomad_canada cspec
PM3	Not assessed	Not assessed: no co-occurrence with a pathogenic MLH1 variant in trans or of unknown phase is reported, so no PM3 points can be assigned.	cspec clinvar gnomad_v4 gnomad_v2
PM4	N/A	Not applicable: the MLH1 VCEP does not use PM4, and this intronic variant causes no protein length change.	cspec
PM5	N/A	Not applicable: the variant is intronic (p.?), not missense, so no same-residue pathogenic comparison is possible.	cspec pm5_candidates
PM6	N/A	Not applicable: de novo evidence is scored only under PS2 in this framework, and none is reported.	cspec
PP1	Not assessed	Not assessed: no pedigrees or carrier/meioses counts exist to compute a co-segregation Bayes likelihood ratio.	cspec clinvar
PP2	N/A	Not applicable: the MLH1 VCEP does not use PP2, and this is not a missense variant.	cspec
PP3	Not met	Not met: SpliceAI max delta 0.00 is well below the >=0.2 PP3 threshold, so no splice defect is predicted.	spliceai cspec vcep_hci_priors_mlh1
PP4	Not assessed	Not assessed: no MSI, MMR IHC, or MLH1 promoter methylation data is available for any carrier.	cspec clinvar
PP5	N/A	Not applicable: the MLH1 VCEP does not use PP5, and ClinVar has zero expert-panel submissions for this variant.	cspec clinvar
BA1	Not met	Not met: gnomAD v4.1 grpmax filtering AF 4.43e-06 is ~226-fold below the >=0.001 BA1 threshold.	gnomad_v4 gnomad_v2 cspec
BS1	Not met	Not met: gnomAD v4.1 grpmax filtering AF 4.43e-06 is below the 0.0001 lower bound of the BS1 window.	gnomad_v4 gnomad_v2 cspec
BS2	Not met	Not met: no in-trans co-occurrence with a pathogenic MLH1 variant is reported, and gnomAD shows zero homozygotes.	cspec gnomad_v4 gnomad_v2 gnomad_canada
BS3	Not assessed	Not assessed: no mRNA (with NMD inhibition) or calibrated functional assay data exists; in silico SpliceAI predictions do not satisfy BS3.	cspec vcep_functional_assay_svi_documentation_mmr spliceai vcep_vcep_pilot_variants_mmr clinvar
BS4	Not assessed	Not assessed: no pedigrees or non-segregation observations exist to compute a likelihood ratio.	cspec clinvar
BP1	N/A	Not applicable: missense variants are an established Lynch syndrome mechanism in MLH1, so BP1 does not apply.	cspec
BP2	N/A	Not applicable: the MLH1 VCEP replaces BP2 with BS2, and no in-trans or in-cis co-occurrence is reported.	cspec
BP3	N/A	Not applicable: the MLH1 VCEP does not use BP3, and this is a single-nucleotide intronic substitution, not an in-frame indel.	cspec
BP4	Met	Met (Supporting): SpliceAI max delta 0.00 is at or below the <=0.1 BP4 threshold, predicting no splicing impact.	spliceai cspec
BP5	Not assessed	Not assessed: no MSI, MMR IHC, BRAF V600E, or MLH1 promoter methylation data exists to show an alternate molecular basis.	cspec clinvar
BP6	N/A	Not applicable: the MLH1 VCEP does not use BP6, and ClinVar's Likely Benign calls are ordinary laboratory submissions, not expert-panel.	cspec clinvar
BP7	Not met	Not met: at donor position +4, the variant is not "at or beyond +7", so the BP7 positional requirement fails.	cspec

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.