LYFE Sciences · Project HERA
Variant Interpretation · Classification Report
Generated: 2026-08-21
Case ID: NM_000249.4_c.549T_A_20260821_142448
Framework: ACMG/AMP 2015
Variant classification summary

NM_000249.4:c.549T>A

MLH1  · NP_000240.1:p.(Tyr183Ter)  · NM_000249.4
GRCh37: chr3:37053314 T>A  ·  GRCh38: chr3:37011823 T>A
Gene: MLH1 Transcript: NM_000249.4
Final call
VUS
PVS1 very strong PM2 supporting
All criteria require review: For research and educational purposes only.
Variant details
Gene
MLH1
Transcript
NM_000249.4
Protein
NP_000240.1:p.(Tyr183Ter)
gnomAD AF
ClinVar
Likely benign
OncoKB
Likely Oncogenic
Classification rationale
Interpretation summary
Generated evidence synthesis
1
NM_000249.4:c.549T>A is a nonsense variant predicted to introduce a premature termination codon at codon 183 (p.Tyr183Ter) in MLH1, a gene in which loss of function is an established cause of Lynch syndrome.
2
Per the InSiGHT MLH1 VCEP, a nonsense/frameshift variant introducing a premature termination codon at or before codon 753 meets PVS1 at very strong strength.
3
This variant has not been observed in gnomAD v2.1 or v4.1, meeting the InSiGHT MLH1 VCEP PM2_Supporting criterion.
4
No ClinVar expert-panel classification exists for this variant; the only retrieved ClinVar record was a mismatched c.1272T>A entry and therefore carries no weight for PP5/BP6 (which are not applicable in this VCEP).
5
PVS1 at very strong strength is independently sufficient for a Pathogenic classification under the InSiGHT MLH1 VCEP combination rules (Rule 1: one very strong pathogenic criterion).
Final determination: No criteria-combination rule matched the adjudicated criteria in the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MLH1 Version 2.0 v2.0 framework, so the variant remains a Variant of Uncertain Significance pending human review.
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 NM_000249.4:c.549T>A is a nonsense variant that introduces a premature termination codon at codon 183 (p.Tyr183Ter), well before the MLH1 cutoff of codon 753, and loss of function is an established disease mechanism for MLH1 in Lynch syndrome; this satisfies PVS1 at very strong strength per the InSiGHT MLH1 VCEP.
cspec pvs1_gene_context pvs1_variant_assessment
PS1 N/A PS1 applies to missense substitutions encoding the same amino acid change or to variants at the same non-canonical splice nucleotide; this is a nonsense variant, so PS1 does not apply.
cspec
PS2 Not met No de novo occurrence of this variant with confirmed maternity and paternity has been reported in the available evidence.
PS3 Not met No calibrated functional assay or variant-specific functional study of p.Tyr183Ter was identified; the reviewed publications describe MLH1 function at the gene or domain level only.
PMID:10359802 PMID:11781295 PMID:12697830
PS4 N/A PS4 is not utilized for MMR variant classification by the InSiGHT MLH1 VCEP because tumor IHC data (PP4) is used instead of proband counting.
cspec
PS5 N/A PS5 is not defined in the InSiGHT MLH1 VCEP framework (not a standard criterion for this gene), so it cannot be applied.
cspec
PM1 N/A PM1 is not applicable for MLH1 in the InSiGHT VCEP because there are no recognized mutational hotspots suitable for classification.
cspec
PM2 Met The variant is absent from gnomAD v2.1 and v4.1, meeting the InSiGHT MLH1 VCEP PM2_Supporting threshold of an allele frequency below 0.00002 (fewer than 1 in 50,000 alleles).
gnomad_v2 gnomad_v4 cspec
PM5 N/A PM5 requires a missense change at a residue where a different missense change is pathogenic; this is a nonsense variant, so PM5 does not apply.
cspec
PM6 N/A PM6 (assumed de novo without confirmation of parentage) is not applicable in the InSiGHT MLH1 VCEP; PS2 is used instead.
cspec
PP1 Not met No co-segregation data are available for this variant.
PP2 N/A PP2 (missense variant in a gene with a low rate of benign missense variation) is not applicable in the InSiGHT MLH1 VCEP.
cspec
PP3 N/A PP3 in the InSiGHT MLH1 VCEP applies only to missense variants (HCI prior) and non-canonical splice variants (SpliceAI delta >= 0.2); this is a nonsense variant and SpliceAI predicts no splicing impact (max delta score 0.014).
cspec spliceai
PP4 Not met No tumor microsatellite instability (MSI) or MMR protein immunohistochemistry data are available for this variant to support PP4.
PP5 N/A PP5 is not applicable in the InSiGHT MLH1 VCEP; additionally, no ClinVar expert-panel classification exists for this variant (the only retrieved ClinVar record was a mismatched c.1272T>A entry).
cspec clinvar
BA1 Not met The variant is absent from gnomAD, so it does not meet the BA1 allele frequency threshold (>= 0.001 in gnomAD v4).
gnomad_v4
BS1 Not met The variant is absent from gnomAD, so it does not meet the BS1 allele frequency threshold (>= 0.0001 and < 0.001 in gnomAD v4).
gnomad_v4
BS2 Not met No observation of this variant in trans with a known pathogenic MLH1 variant in a patient without CMMRD has been reported.
BS3 Not met No functional assay demonstrating normal (proficient) protein function for p.Tyr183Ter was identified; the reviewed publications are gene-level studies only.
PMID:10359802 PMID:11781295 PMID:12697830
BS4 Not met No segregation data demonstrating lack of co-segregation with disease are available.
BP1 N/A BP1 (missense variant in a gene where primarily truncating variants cause disease) is not applicable in the InSiGHT MLH1 VCEP.
cspec
BP2 N/A BP2 is not applicable in the InSiGHT MLH1 VCEP; BS2 is used instead.
cspec
BP4 N/A BP4 in the InSiGHT MLH1 VCEP applies only to missense variants (HCI prior < 0.11) and intronic/synonymous variants (SpliceAI <= 0.1); this is a nonsense coding variant, so BP4 does not apply.
cspec spliceai
BP5 Not met No tumor data (MSS tumors, no loss of MMR protein expression, BRAF V600E, or MLH1 promoter methylation) are available to support BP5.
BP6 N/A BP6 is not applicable in the InSiGHT MLH1 VCEP; additionally, no ClinVar expert-panel classification exists for this variant.
cspec clinvar
BP7 N/A BP7 applies only to synonymous or intronic variants; this is a nonsense (stop-gain) coding variant.
cspec
BP3 N/A BP3 applies to in-frame deletions/insertions in a repetitive region; this is a single-nucleotide nonsense substitution.
PM3 N/A PM3 requires biallelic in trans co-occurrence with a pathogenic variant in a recessive (CMMRD) context, which is not the setting for this dominant Lynch syndrome case.
PM4 N/A PM4 applies to protein length changes from in-frame insertions/deletions or stop-loss; this is a nonsense (stop-gain) substitution and PM4 is not used in the InSiGHT MLH1 VCEP.
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