NM_000179.3:c.643G>C (p.Val215Leu) is a missense variant in exon 4 of MSH6. It is extremely rare in population databases (gnomAD v4.1 AF=1.24e-06), meeting PM2_Supporting per the InSiGHT MSH6 VCEP v2.0.0 threshold of <0.00002.1 Multiple in silico predictors support a benign effect: the MSH6-specific HCI prior probability for pathogenicity is 0.0008, meeting BP4_Supporting (threshold <0.11). REVEL (0.139) and BayesDel (-0.503783) are also consistent with a benign prediction. SpliceAI predicts no splicing impact (max delta 0.09).2 No variant-specific functional data, segregation data, tumor phenotype data, or de novo observations are available for this variant. The variant has not been classified by the VCEP pilot program and no comparator missense changes at codon 215 have been established as pathogenic.3 This variant has been reported in ClinVar as Uncertain Significance by multiple clinical laboratories (ClinVar ID: 628619). Nine publications were reviewed; none mention NM_000179.3:c.643G>C.4
MSH6
Final classification
Uncertain Significance - Conflicting Evidence
MSH6 c.643G>C · p.Val215Leu
MSH6
NM_000179.3:c.643G>C (p.Val215Leu) is a missense variant in exon 4 of MSH6. It is extremely rare in population databases (gnomAD v4.1 AF=1.24e-06), meeting PM2_Supporting per the InSiGHT MSH6 VCEP v2.0.0 threshold of <0.00002.
ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH6 Version 2.0.0 v2.0.0 criteria-combination framework: matched Rule31 (Benign.Supporting >=1 + Pathogenic.Supporting >=1) with applied criteria: PM2 supporting, BP4 supporting benign; maps to Uncertain Significance - Conflicting Evidence.
Classification rationale
PM2
BP4
Uncertain Significance - Conflicting Evidence
MSH6 c.643G>C
PM2 + BP4
→
Uncertain Significance - Conflicting Evidence
2
hci_priorrevelbayesdelspliceai ↗
3
clinvar ↗vcep_functional_assay_svi_documentation_mmrvcep_vcep_pilot_variants_mmr
Gene diagram
· NM_000179.3 · variants mapped to exon structure
MSH6
NM_000179.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 13 assessed
Applied · 2
Strength
Supporting
Moderate
Strong
Very strong
✓
PM2
supporting
Pathogenic
NM_000179.3:c.643G>C is extremely rare in population databases. In gnomAD v4.1, the allele frequency is 1.24e-06 (2/1,610,788 alleles, no homozygotes), which is below the VCEP PM2 threshold of <0.00002 (<1 in 50,000 alleles).
gnomAD v4.1: AF=1.24e-06 (2/1610788 alleles).
✓
BP4
supporting
Benign
Multiple computational predictors support a benign effect. The MSH6-specific HCI prior probability for pathogenicity is 0.0008, which falls below the VCEP BP4_Supporting threshold of <0.11. SpliceAI predicts no splicing impact (max delta score = 0.09, ≤0.1). REVEL score is 0.139 and BayesDel score is -0.503783, both consistent with a benign prediction.
HCI prior=0.0008 (<0.11)SpliceAI delta=0.09 (≤0.1)REVEL=0.139
Assessed · not applied
Pathogenic
PS1
No nucleotide change encoding p.Val215Leu has been previously classified as Pathogenic or Likely Pathogenic by this VCEP.
PS2
No de novo observations are reported in ClinVar or the literature for NM_000179.3:c.643G>C.
PS3
No variant-specific functional assay data for NM_000179.3:c.643G>C were identified in the VCEP functional assay documentation or in the reviewed literature.
PM5
No different missense change at codon 215 (Val215) has been classified as Pathogenic or Likely Pathogenic by this VCEP.
PP1
No co-segregation data are available for NM_000179.3:c.643G>C.
PP3
Multiple in silico predictors indicate a benign effect.
PP4
No MSI-H tumor data with MMR protein expression loss consistent with an MSH6 defect are reported for this variant.
Benign
BA1
The gnomAD v4.1 allele frequency of 1.24e-06 (0.000124%) is far below the VCEP BA1 Stand-Alone threshold of ≥0.0022 (0.22%).
BS1
The gnomAD v4.1 allele frequency of 1.24e-06 (0.000124%) is below the VCEP BS1 Strong threshold of ≥0.00022 (0.022%).
BS2
No observation of this variant in trans with a known pathogenic MSH6 variant in a patient with CRC after age 45 without CMMRD features has been reported.
BS3
No variant-specific functional assay data demonstrating benign or normal function for NM_000179.3:c.643G>C are available.
BS4
No co-segregation data are available to assess lack of segregation with disease for NM_000179.3:c.643G>C.
BP5
No tumor data demonstrating MSS status or inconsistent MMR protein expression are available for this variant.
N/A · 10
PVS1 · PS4 · PM1 · PM6 · PP2 · PP5 · BP1 · BP2 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 1.24163e-06; MAF= 0.00012%, 2/1610788 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 2.22727e-05; MAF= 0.00223%, 1/44898 alleles, homozygotes = 0).
v2.1
This variant is present in gnomAD v2.1 (AF= 4.05108e-06; MAF= 0.00041%, 1/246848 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.87737e-06; MAF= 0.00089%, 1/112646 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00012%
· 2 / 1,610,788
0 hom
0 hom
East Asian 1 / 44,898 |
0.0022% |
European (non-Finnish) 1 / 1,179,946 |
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
0.00041%
· 1 / 246,848
0 hom
0 hom
European (non-Finnish) 1 / 112,646 |
0.00089% |
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, 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 Uncertain significance (3 clinical laboratories) and as Uncertain Significance (1 clinical laboratory) and as Likely benign (1 clinical laboratory). (ClinVarID = 628619)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.09). REVEL score = 0.139. BayesDel score = -0.503783. HCI prior probability for pathogenicity = 0.0008. MAPP score = 2.5. Custom PP2 score = 0.0.
Functional
Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. MSH6, a DNA mismatch repair protein, is frequently mutated in colorectal, small bowel, and endometrial cancers.
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 · 9 PMIDs not cited in assessment
25070057 ↗
Guidelines on genetic evaluation and management of Lynch syndrome: a consensus statement by the US Multi-society Task Force on colorectal cancer.
CLINVAR
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
23408351 ↗
Revised guidelines for the clinical management of Lynch syndrome (HNPCC): recommendations by a group of European experts.
CLINVAR
24310308 ↗
ACMG technical standards and guidelines for genetic testing for inherited colorectal cancer (Lynch syndrome, familial adenomatous polyposis, and MYH-associated polyposis).
CLINVAR
27854360 ↗
Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics.
CLINVAR
28492532 ↗
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
CLINVAR