LYFE Sciences · Project HERA
Variant Interpretation · Classification Report
Generated: 2026-05-06
Case ID: NM_000249.4_c.1039-6dup_20260506_174934
Framework: ACMG/AMP 2015
Variant classification summary

NM_000249.4:c.1039-6dup

MLH1  · NP_000240.1:p.?  · NM_000249.4
GRCh37: chr3:37067120 T>TA  ·  GRCh38: chr3:37025629 T>TA
Gene: MLH1 Transcript: NM_000249.4
Final call
Benign
BA1 stand-alone benign BP4 supporting
All criteria require review: For research and educational purposes only.
Variant details
Gene
MLH1
Transcript
NM_000249.4
Protein
NP_000240.1:p.?
gnomAD AF
ClinVar
OncoKB
Classification rationale
Interpretation summary
Generated evidence synthesis
1
The MLH1 c.1039-6dup (p.?) variant has been reported in ClinVar as benign by 5 clinical laboratories and likely benign by 4 clinical laboratories.
2
This variant is present in population databases; in gnomAD v4.1 the overall allele frequency is 0.000530357 and the grpmax filtering allele frequency is 0.00117106, which is above the MLH1 VCEP BA1 threshold of 0.001.
3
SpliceAI predicts no significant splice effect, with a maximum delta score of 0.01, which is below the BP4 no-impact threshold of 0.1 and below the PP3 splice-defect threshold of 0.2 in the MLH1 VCEP rules.
Final determination: Rule17 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 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
BA1 Met This variant is present in gnomAD v4.1 with a grpmax filtering allele frequency of 0.00117106, which is above the MLH1 VCEP BA1 threshold of 0.001.
gnomad_v4 cspec
BP1 N/A BP1 is not applicable in this MLH1 VCEP framework.
cspec
BP2 N/A BP2 is not applicable in this MLH1 VCEP framework.
cspec
BP3 N/A BP3 is not applicable in this MLH1 VCEP framework.
cspec
BP4 Met SpliceAI predicts no significant splice impact for this intronic variant, with a maximum delta score of 0.01, which is below the MLH1 VCEP BP4 threshold of 0.1 for no predicted splicing effect.
spliceai cspec
BP5 Not assessed No tumor-based evidence was identified showing microsatellite stable disease, retained mismatch repair protein expression, inconsistent mismatch repair protein loss, or MLH1 methylation/BRAF findings sufficient for BP5.
cspec
BP6 N/A BP6 is not applicable in this MLH1 VCEP framework.
cspec
BP7 Not met This intronic variant is located at c.1039-6, which is closer to the splice acceptor than the MLH1 VCEP BP7 boundary of at or beyond -21 for intronic variants, so BP7 is not met.
cspec
BS1 Not met The gnomAD v4.1 grpmax filtering allele frequency is 0.00117106, which is above the BS1 range upper limit of less than 0.001, so BS1 is not the appropriate population criterion.
gnomad_v4 cspec
BS2 Not assessed No confirmed in trans observation with a pathogenic mismatch repair variant in an individual lacking clinical evidence of constitutional mismatch repair deficiency was identified.
cspec vcep_table_for_cmmrd_diagnosis
BS3 Not assessed No RNA assay or other functional study was identified showing normal splicing or preserved mismatch repair function for this variant.
cspec vcep_functional_assay_flowchart vcep_functional_assay_svi_documentation_mmr
BS4 Not assessed No informative family data were identified showing lack of segregation of this variant with disease.
cspec
PVS1 Not met Loss of function is an established MLH1 disease mechanism, but this c.1039-6dup change is a non-canonical intronic variant rather than a canonical ±1/2 splice-site or other default null variant, and no RNA evidence was identified showing a splice defect sufficient for PVS1.
cspec pvs1_gene_context pvs1_variant_assessment
PM1 N/A PM1 is not applicable in this MLH1 VCEP framework.
cspec
PM2 Not met This variant is not absent or extremely rare in gnomAD v4.1; its overall allele frequency is 0.000530357, which is above the MLH1 VCEP PM2_Supporting threshold of less than 0.00002.
gnomad_v4 cspec
PM3 Not assessed No evidence was identified that this variant was observed with another pathogenic mismatch repair variant in trans in a patient with features consistent with constitutional mismatch repair deficiency.
cspec vcep_table_for_cmmrd_diagnosis
PM4 N/A PM4 is not applicable in this MLH1 VCEP framework.
cspec
PM5 N/A PM5 is defined here for missense substitutions, and this variant is a non-canonical intronic duplication rather than a missense change.
cspec
PM6 N/A PM6 is not applicable in this MLH1 VCEP framework.
cspec
PP1 Not assessed No segregation data were identified for this variant.
cspec
PP2 N/A PP2 is not applicable in this MLH1 VCEP framework.
cspec
PP3 Not met SpliceAI does not support a predicted splice defect for this non-canonical intronic variant; the maximum delta score is 0.01, which is below the MLH1 VCEP PP3 threshold of 0.2. HCI prior, REVEL, and BayesDel are not applicable because this is not a missense single-nucleotide substitution.
spliceai cspec
PP4 Not assessed No tumor microsatellite instability or mismatch repair immunohistochemistry data were identified to support a Lynch syndrome-specific tumor phenotype for this variant.
cspec
PP5 N/A PP5 is not applicable in this MLH1 VCEP framework.
cspec
PS1 Not assessed This is a non-canonical splice-region variant, but no evidence was identified that another pathogenic or likely pathogenic variant affecting the same non-canonical splice nucleotide has similar or stronger predicted splicing impact.
cspec spliceai
PS2 Not assessed No de novo occurrence with confirmed parentage was identified for this variant.
cspec
PS3 Not assessed No functional assay or patient RNA study was identified showing that this variant causes an abnormal MLH1 transcript or mismatch repair defect at a VCEP-qualified strength.
cspec vcep_functional_assay_flowchart vcep_functional_assay_svi_documentation_mmr
PS4 N/A PS4 is not applicable in this MLH1 VCEP framework.
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.