NM_000249.4:c.1515T>C is a synonymous variant (p.Ser505=) in MLH1 exon 13, located well beyond splice consensus boundaries at c.1515 (+105 from donor, -43 from acceptor). SpliceAI predicts no splicing impact for this variant (max delta score = 0.00), meeting BP4_supporting under the InSiGHT MLH1 VCEP specification.1 The variant meets BP7_supporting as a synonymous substitution at or beyond -21/+7 from exonic splice boundaries, where it is unlikely to alter splicing. The variant is present in gnomAD v4.1 at low frequency (grpmax FAF = 2.978e-05; 5/1,614,044 alleles) but does not meet PM2_supporting (threshold <0.00002) or BS1 (threshold ≥0.0001).2 No functional data, tumor pathology data, co-segregation data, de novo observations, or variant-specific literature were identified for this variant. This variant has been reported in ClinVar as Likely benign by 7 clinical laboratories (ClinVar Variation ID: 413362).3 Under the InSiGHT MLH1 VCEP v2.0.0 combining rules, two supporting benign criteria (BP4 + BP7) yield a classification of Likely Benign (Rule 19: ≥2 Benign Supporting).4
MLH1
Final classification
Likely Benign
MLH1 c.1515T>C · p.Ser505=
MLH1
NM_000249.4:c.1515T>C is a synonymous variant (p.Ser505=) in MLH1 exon 13, located well beyond splice consensus boundaries at c.1515 (+105 from donor, -43 from acceptor).
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: matched Rule19 (Benign.Supporting >=2) with applied criteria: BP4 supporting benign, BP7 supporting benign; maps to Likely Benign.
Classification rationale
BP4BP7
Likely Benign
MLH1 c.1515T>C
BP4 + BP7
→
Likely Benign
Gene diagram
· NM_000249.4 · variants mapped to exon structure
MLH1
NM_000249.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 12 assessed
Applied · 2
Strength
Supporting
Moderate
Strong
Very strong
✓
BP4
supporting
Benign
VCEP BP4 specifies that for synonymous variants, SpliceAI delta score ≤ 0.1 qualifies as BP4_supporting. SpliceAI predicts no splicing impact (max delta = 0.00), consistent with a synonymous variant that does not alter splicing.
SpliceAI max delta = 0.00 for NM_000249.4:c.1515T>Csynonymous variant with no predicted splice impact
✓
BP7
supporting
Benign
VCEP BP7 applies to synonymous (silent) variants at or beyond -21/+7 from exonic splice boundaries. NM_000249.4:c.1515T>C (p.Ser505=) is a synonymous variant located at position +105 from the exon 13 donor splice site and -43 from the exon 13 acceptor splice site, both well beyond the -21/+7 splice consensus boundaries. This deep exonic synonymous substitution is unlikely to affect splicing.
Synonymous variant p.(Ser505=) at c.1515 in exon 13position +105 from donor-43 from acceptor
Assessed · not applied
Pathogenic
PS2
No de novo observations have been reported for this variant.
PS3
No functional data are available for this synonymous variant (p.Ser505=).
PM2
VCEP PM2 rule requires gnomAD v4 grpmax filtering allele frequency < 0.00002 (<1 in 50,000 alleles).
PP1
No co-segregation data are available for this variant.
PP3
VCEP PP3 requires HCI prior probability >0.68 (missense) or SpliceAI delta ≥ 0.2 for non-canonical splice sites.
PP4
No tumor data demonstrating MSI-H status or loss of MMR protein expression consistent with the variant location are available for this variant.
Benign
BA1
VCEP BA1 requires gnomAD v4 grpmax filtering allele frequency ≥ 0.001 (0.1%).
BS1
VCEP BS1 requires gnomAD v4 grpmax filtering allele frequency ≥ 0.0001 and < 0.001 (0.01-0.1%).
BS2
No evidence of co-occurrence in trans with a known pathogenic variant in a patient with CRC after age 45 without clinical manifestations of CMMRD.
BS3
No functional studies demonstrating a benign effect are available for this variant.
BS4
No lack-of-segregation data are available for this variant.
BP5
No tumor data demonstrating MSS status or absence of MMR protein expression loss are available for this variant.
N/A · 14
PVS1 · PS1 · PS4 · PM1 · PM3 · PM4 · PM5 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP6
Research & evidence
Population frequency · supports benign
gnomAD v4.1
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 3.09781e-06; MAF= 0.00031%, 5/1614044 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 8.91266e-05; MAF= 0.00891%, 4/44880 alleles, homozygotes = 0); grpmax FAF= 2.978e-05.
v2.1
This variant is present in gnomAD v2.1 (AF= 1.98829e-05; MAF= 0.00199%, 5/251472 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 0.000217462; MAF= 0.02175%, 4/18394 alleles, homozygotes = 0); grpmax FAF= 7.353e-05.
🇨🇦 CA
Not available in gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00031%
· 5 / 1,614,044
0 hom · FAF 0.003%
0 hom · FAF 0.003%
East Asian 4 / 44,880 |
0.0089% |
European (non-Finnish) 1 / 1,180,006 |
8.5e-05% |
+ 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.002%
· 5 / 251,472
0 hom · FAF 0.0074%
0 hom · FAF 0.0074%
East Asian 4 / 18,394 |
0.022% |
European (non-Finnish) 1 / 113,748 |
0.00088% |
+ 6 not observed (African/African American, Admixed American, Ashkenazi Jewish, European (Finnish), Remaining individuals, South Asian)
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
ClinVar
This variant has been reported in ClinVar as Likely benign (5 clinical laboratories) and as Likely Benign (1 clinical laboratory) and as Benign (1 clinical laboratory). (ClinVarID = 413362)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.343.
Functional
Unknown Oncogenic Effect
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
COSMIC
Cancer hotspots
Somatic evidence
Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
Triaged references · 7 PMIDs not cited in assessment
25741868 ↗
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
CLINVAR
15604628 ↗
Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors.
CLINVAR
23535968 ↗
Informing family members of individuals with Lynch syndrome: a guideline for clinical geneticists.
CLINVAR
23788249 ↗
ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.
CLINVAR
25356965 ↗
ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing.
CLINVAR
25452455 ↗
Hereditary colorectal cancer syndromes: American Society of Clinical Oncology Clinical Practice Guideline endorsement of the familial risk-colorectal cancer: European Society for Medical Oncology Clinical Practice Guidelines.
CLINVAR
28492532 ↗
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
CLINVAR