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MSH6
Final classification
VUS
MSH6 c.440T>G · p.Leu147Arg
MSH6

NM_000179.2:c.440T>G (p.Leu147Arg) is a missense variant in exon 2 of MSH6.

Gene
MSH6
Transcript
NM_000179.2
HGVS · transcript:coding
NM_000179.2:c.440T>G
Consequence
N/A
GRCh38
chr2:47791106 T>G
GRCh37
chr2:48018245 T>G
Basis 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 was evaluated deterministically with applied criteria: PM2 supporting; no rule matched the adjudicated criteria.
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 was evaluated deterministically with applied criteria: PM2 supporting; no rule matched the adjudicated criteria.
Classification rationale
PM2 VUS
MSH6 c.440T>G

NM_000179.2:c.440T>G (p.Leu147Arg) is a missense variant in exon 2 of MSH6. This variant is extremely rare in population databases, observed in 1 of 1,614,050 alleles in gnomAD v4.1 (AF = 6.20e-07), meeting PM2_Supporting under the InSiGHT MSH6 VCEP framework.1 The variant is classified as Uncertain Significance in ClinVar by 3 clinical laboratories (ClinVar Variation ID: 1740396) with no expert panel submissions.2 No variant-specific functional studies, cosegregation data, de novo observations, or tumor phenotype data were identified in the VCEP functional assay documentation, ClinVar submissions, or published literature.3 In silico predictors are inconclusive: HCI prior probability is 0.3529 (below PP3 thresholds), REVEL score is 0.222, BayesDel is -0.269843, and SpliceAI predicts no splicing impact (delta = 0.01). These do not meet thresholds for PP3 or BP4 under the VCEP framework.4 No same-residue pathogenic comparator variant (PM5) or same-amino-acid nucleotide change comparator (PS1) was identified in the VCEP pilot variants.5 With only PM2_Supporting met, and no benign or additional pathogenic criteria fulfilled, the variant is classified as Uncertain Significance under the InSiGHT MSH6 VCEP v2.0.0 combination rules.6

PM2 VUS
3 vcep_functional_assay_svi_documentation_mmroncokb ↗
4 hci_priorrevelbayesdelspliceai ↗
5 vcep_vcep_pilot_variants_mmrpm5_candidates
6 cspec ↗final_classification_framework
Gene diagram · NM_000179.2 · variants mapped to exon structure
MSH6 NM_000179.2
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 14 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is extremely rare in population databases, with a gnomAD v4.1 allele frequency of 6.20e-07 (1/1,614,050 alleles, 0 homozygotes), which is below the InSiGHT MSH6 VCEP PM2_Supporting threshold of <0.00002 (<1 in 50,000 alleles).
gnomAD v4.1: AF = 6.20e-07 (1/1614050 alleles
Assessed · not applied
Pathogenic
PS1 No prior VCEP classification exists for a different nucleotide change encoding the same amino acid substitution (p.Leu147Arg).
PS2 No de novo occurrence data are available for this variant.
PS3 No variant-specific functional evidence is available for NM_000179.2:c.440T>G.
PM5 No different missense change at the same amino acid residue (Leu147) has been classified by the InSiGHT VCEP as Pathogenic or Likely Pathogenic.
PP1 No cosegregation data are available for this variant.
PP3 The HCI prior probability for this variant is 0.3529, which falls below the InSiGHT MSH6 VCEP thresholds for PP3 (Supporting: >0.68; Moderate: >0.81).
PP4 No tumor-based evidence (MSI-H status, MMR protein IHC, or consistent tumor phenotype) is available for individuals carrying this variant.
Benign
BA1 The gnomAD v4.1 allele frequency (6.20e-07, 0.000062%) is far below the InSiGHT MSH6 VCEP BA1 Stand-Alone threshold of ≥0.0022 (0.22%).
BS1 The gnomAD v4.1 allele frequency (6.20e-07) is below the InSiGHT MSH6 VCEP BS1_Strong lower bound of ≥0.00022 (0.022%).
BS2 No evidence of co-occurrence in trans with a known pathogenic MSH6 variant in a patient meeting the VCEP clinical criteria (colorectal cancer after age 45 without CMMRD features) has been reported.
BS3 No variant-specific functional evidence supporting a benign effect is available.
BS4 No lack-of-cosegregation data are available.
BP4 The HCI prior probability for this variant is 0.3529, which exceeds the InSiGHT MSH6 VCEP BP4_Supporting threshold of <0.11.
BP5 No tumor-based evidence supporting a benign interpretation is available.
N/A · 11 PVS1 · PS4 · PM1 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 6.19559e-07; MAF= 0.00006%, 1/1614050 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 1.33465e-05; MAF= 0.00133%, 1/74926 alleles, homozygotes = 0).
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
6.2e-05% · 1 / 1,614,050
0 hom
African/African American
1 / 74,926
0.0013%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, European (non-Finnish))
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (3 clinical laboratories). (ClinVarID = 1740396)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.222. BayesDel score = -0.269843. HCI prior probability for pathogenicity = 0.3529. MAPP score = 24.22. Custom PP2 score = 0.319.
Functional / OncoKB screenshot
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.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
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
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 6 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
20301390 ↗ Lynch Syndrome. CLINVAR
24493721 ↗ American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers. CLINVAR
34012068 ↗ ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG). CLINVAR
24905773 ↗ Endometrial cancer: a review and current management strategies: part I. CLINVAR
24929052 ↗ Endometrial cancer: a review and current management strategies: part II. CLINVAR