Variant classification summary

NM_000249.4:c.688G>C

MLH1 · NP_000240.1:p.(Glu230Gln) · NM_000249.4

GRCh37: chr3:37055933 G>C · GRCh38: chr3:37014442 G>C

Gene: MLH1 Transcript: NM_000249.4

Final call

PM2 supporting BP4 supporting

Variant details

Gene

MLH1

Transcript

NM_000249.4

Protein

NP_000240.1:p.(Glu230Gln)

gnomAD AF

1.2682726380324526e-06 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

The MLH1 NM_000249.4:c.688G>C (p.Glu230Gln; p.E230Q) variant has been reported in ClinVar as a variant of uncertain significance with four clinical laboratory submissions.

2

This variant is present at very low frequency in population databases, including gnomAD v4.1 at 2/1576948 alleles (AF 1.26827e-06; grpmax FAF 2.9e-07) and gnomAD v2.1 at 1/31410 alleles (AF 3.1837e-05), which is below the MLH1 PM2_Supporting threshold of 0.00002 in gnomAD v4.

3

No variant-specific calibrated functional assay result for p.Glu230Gln was identified in the reviewed mismatch repair functional assay references.

4

For this MLH1 missense variant, the HCI prior probability is 0.0581, below the BP4 threshold of 0.11; REVEL is 0.627, BayesDel is 0.158729, and SpliceAI predicts no significant splice impact with a maximum delta score of 0.04.

Final determination: Rule31 in the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MLH1 Version 2.0.0 v2.0.0 criteria-combination framework is satisfied by the adjudicated criteria, so the variant is classified as Uncertain Significance - Conflicting Evidence.

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	This is a missense substitution, not a nonsense, frameshift, canonical +/-1,2 splice, initiation codon, or proven splice-abrogating variant, so PVS1 is not met under the MLH1-specific rules.	cspec pvs1_gene_context pvs1_variant_assessment
PS1	Not assessed	No previously established MLH1 pathogenic or likely pathogenic variant causing the same amino acid change with a different nucleotide change was identified in the available evidence, so PS1 was not applied.	clinvar cspec
PS2	Not assessed	No confirmed de novo occurrence data with the point-based evidence required by the MLH1 VCEP were identified, so PS2 was not assessed.	cspec
PS3	Not assessed	No variant-specific calibrated functional assay result for p.Glu230Gln was identified in the reviewed mismatch repair functional assay references, so PS3 was not applied.	vcep_functional_assay_svi_documentation_mmr oncokb cspec
PS4	N/A	PS4 is not used in the MLH1 VCEP specification for this gene framework.	cspec
PM1	N/A	PM1 is not used in the MLH1 VCEP specification for this gene framework.	cspec
PM2	Met	This variant is present at very low frequency in gnomAD v4.1 at 2/1576948 alleles (AF 1.26827e-06), which is below the MLH1 PM2_Supporting threshold of 0.00002.	gnomad_v4 cspec
PM3	Not assessed	No confirmed in trans observations with an established pathogenic MLH1 variant and no PM3 point-based evidence were identified, so PM3 was not assessed.	cspec
PM4	N/A	PM4 is not used in the MLH1 VCEP specification for this gene framework.	cspec
PM5	Not assessed	No eligible same-residue pathogenic or likely pathogenic missense comparator at codon 230 was established from the available evidence, so PM5 was not applied.	pm5_candidates vcep_vcep_pilot_variants_mmr cspec
PM6	N/A	PM6 is not used in the MLH1 VCEP specification for this gene framework.	cspec
PP1	Not assessed	No segregation data with a calculable Bayes likelihood ratio were identified, so PP1 was not assessed.	cspec
PP2	N/A	PP2 is not used in the MLH1 VCEP specification for this gene framework.	cspec
PP3	Not met	For this MLH1 missense variant, the HCI prior probability is 0.0581, which is below the PP3 thresholds of >0.68 for Supporting and >0.81 for Moderate. REVEL is 0.627 and BayesDel is 0.158729, but the MLH1 VCEP prioritizes the HCI prior for missense PP3/BP4. SpliceAI also predicts no significant splice impact, with a maximum delta score of 0.04, which is below the non-canonical splice PP3 threshold of 0.2.	hci_prior revel bayesdel spliceai cspec
PP4	Not assessed	No tumor MSI, mismatch repair immunohistochemistry, or MLH1 promoter methylation data were identified to support the MLH1-specific PP4 phenotype rule, so PP4 was not assessed.	cspec
PP5	N/A	PP5 is not used in the MLH1 VCEP specification for this gene framework.	cspec
BA1	Not met	The gnomAD v4.1 grpmax filtering allele frequency is 2.9e-07, which is below the BA1 threshold of 0.001, so BA1 is not met.	gnomad_v4 cspec
BS1	Not met	The gnomAD v4.1 grpmax filtering allele frequency is 2.9e-07, which is below the BS1 range of 0.0001 to <0.001, so BS1 is not met.	gnomad_v4 cspec
BS2	Not assessed	No confirmed in trans co-occurrence with a known pathogenic MLH1 variant in an individual meeting the MLH1 VCEP BS2 conditions was identified, so BS2 was not assessed.	cspec
BS3	Not assessed	No variant-specific calibrated functional evidence showing retained mismatch repair function was identified in the reviewed functional assay references, so BS3 was not applied.	vcep_functional_assay_svi_documentation_mmr oncokb cspec
BS4	Not assessed	No non-segregation data with a calculable Bayes likelihood ratio were identified, so BS4 was not assessed.	cspec
BP1	N/A	BP1 is not used in the MLH1 VCEP specification for this gene framework.	cspec
BP2	N/A	BP2 is not used in the MLH1 VCEP specification for this gene framework.	cspec
BP3	N/A	BP3 is not used in the MLH1 VCEP specification for this gene framework.	cspec
BP4	Met	For this MLH1 missense variant, the HCI prior probability is 0.0581, which is below the BP4 threshold of 0.11 and supports BP4_Supporting. REVEL is 0.627 and BayesDel is 0.158729, and SpliceAI predicts no significant splice impact with a maximum delta score of 0.04.	hci_prior revel bayesdel spliceai cspec
BP5	Not assessed	No tumor findings meeting the MLH1-specific BP5 conditions, such as multiple MSS or inconsistent mismatch repair protein results or qualifying MLH1 methylation/BRAF evidence, were identified, so BP5 was not assessed.	cspec
BP6	N/A	BP6 is not used in the MLH1 VCEP specification for this gene framework.	cspec
BP7	N/A	BP7 is restricted to synonymous or qualifying intronic variants, and this variant is a missense substitution.	cspec

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