Variant classification summary

NM_000249.4:c.1515T>C

MLH1 · NP_000240.1:p.(Ser505=) · NM_000249.4

GRCh37: chr3:37070380 T>C · GRCh38: chr3:37028889 T>C

Gene: MLH1 Transcript: NM_000249.4

Final call

Likely Benign

BP4 supporting BP7 supporting

Variant details

Gene

MLH1

Transcript

NM_000249.4

Protein

NP_000240.1:p.(Ser505=)

gnomAD AF

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

The MLH1 c.1515T>C (p.Ser505=) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar predominantly as likely benign or benign.

2

This variant is present in gnomAD, including 5/1614044 alleles overall in v4.1 (AF 0.00000310) and 4/44880 East Asian alleles (AF 0.0000891), with a grpmax filtering allele frequency of 0.0000298 that is below the BA1 and BS1 thresholds.

3

In silico splicing analysis predicts no significant splice impact with a SpliceAI max delta score of 0.00, supporting BP4 for a synonymous variant; no MLH1 HCI prior entry for c.1515T>C was identified, and the available REVEL score was 0.343.

Final determination: Rule19 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 Likely Benign.

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 synonymous variant does not create a premature stop, frameshift, canonical ±1,2 splice-site, or initiation codon change. SpliceAI predicts no splice effect (max delta score 0.00), and no RNA evidence showing loss of the full-length transcript was identified, so PVS1 is not met.	cspec spliceai pvs1_gene_context pvs1_variant_assessment
PS1	N/A	This variant is synonymous and does not create a missense substitution, and no evidence was identified that it affects the same non-canonical splice nucleotide as an established pathogenic or likely pathogenic splice variant. PS1 is not applicable.	cspec
PS2	Not assessed	No confirmed de novo occurrence with appropriate parental testing was identified, so PS2 cannot be assessed from the available evidence.	cspec
PS3	Not assessed	No calibrated functional assay or variant-specific RNA study demonstrating a damaging effect was identified, so PS3 cannot be assessed.	cspec vcep_functional_assay_svi_documentation_mmr
PS4	N/A	PS4 is not used in this VCEP framework for this case.	cspec
PM1	N/A	PM1 is not used in this VCEP framework for this case.	cspec
PM2	Not met	This variant is rare in gnomAD v4.1 overall (5/1614044 alleles; AF 0.00000310), but the highest observed East Asian frequency is 4/44880 alleles (AF 0.0000891), which is above the PM2 threshold of 0.00002. Available population data therefore do not support applying PM2.	cspec gnomad_v4
PM3	Not assessed	No confirmed in trans occurrence with a pathogenic or likely pathogenic MLH1 variant in a patient meeting the required CMMRD context was identified, so PM3 cannot be assessed.	cspec vcep_table_for_cmmrd_diagnosis
PM4	N/A	PM4 is not used in this VCEP framework for this case.	cspec
PM5	N/A	This variant is synonymous and does not create a missense substitution, so PM5 is not applicable.	cspec
PM6	N/A	PM6 is not used in this VCEP framework for this case.	cspec
PP1	Not assessed	No segregation data were identified to show that this variant tracks with Lynch syndrome-related disease in informative relatives, so PP1 cannot be assessed.	cspec
PP2	N/A	PP2 is not used in this VCEP framework for this case.	cspec
PP3	Not met	This variant is not a missense substitution, SpliceAI predicts no splice defect (max delta score 0.00, below the PP3 threshold of 0.2), and no MLH1 HCI prior entry for c.1515T>C was identified. Available computational evidence does not support PP3.	cspec spliceai vcep_hci_priors_mlh1
PP4	Not assessed	No tumor MSI or mismatch repair immunohistochemistry evidence, and no MLH1 promoter methylation exclusion data, were identified to support PP4.	cspec
PP5	N/A	PP5 is not used in this VCEP framework for this case.	cspec
BA1	Not met	The gnomAD v4.1 grpmax filtering allele frequency is 0.0000298, which is below the BA1 threshold of 0.001. BA1 is not met.	cspec gnomad_v4
BS1	Not met	The gnomAD v4.1 grpmax filtering allele frequency is 0.0000298, which is below the BS1 threshold range of 0.0001 to <0.001. BS1 is not met.	cspec gnomad_v4
BS2	Not assessed	No phase-confirmed co-occurrence with a known pathogenic MLH1 variant in the required clinical setting was identified, so BS2 cannot be assessed.	cspec vcep_table_for_cmmrd_diagnosis
BS3	Not assessed	No variant-specific RNA study showing normal splicing or calibrated functional evidence showing no damaging effect was identified, so BS3 cannot be assessed.	cspec vcep_functional_assay_svi_documentation_mmr
BS4	Not assessed	No informative non-segregation data were identified, so BS4 cannot be assessed.	cspec
BP1	N/A	BP1 is not used in this VCEP framework for this case.	cspec
BP2	N/A	BP2 is not used in this VCEP framework for this case.	cspec
BP3	N/A	BP3 is not used in this VCEP framework for this case.	cspec
BP4	Met	For this synonymous variant, SpliceAI predicts no splicing impact with a max delta score of 0.00, which is below the BP4 threshold of 0.1. A REVEL score of 0.343 was present, but the MLH1 VCEP benign computational rule for synonymous variants is based on SpliceAI; no MLH1 HCI prior entry for c.1515T>C was identified. BP4 is met at supporting strength.	cspec spliceai revel vcep_hci_priors_mlh1
BP5	Not assessed	No tumor findings such as MSS status, discordant mismatch repair protein loss, BRAF V600E, or MLH1 methylation were identified to support BP5.	cspec
BP6	N/A	BP6 is not used in this VCEP framework for this case.	cspec
BP7	Met	This is a synonymous MLH1 variant in exon 13 and is not within the first 21 exonic bases or last 7 exonic bases of the exon, so it falls beyond the BP7 boundary of -21/+7. BP7 is met at supporting strength.	cspec

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