Variant classification summary

NM_000179.3:c.533G>T

MSH6 · NP_000170.1:p.(Arg178Leu) · NM_000179.3

GRCh37: chr2:48023108 G>T · GRCh38: chr2:47795969 G>T

Gene: MSH6 Transcript: NM_000179.3

Final call

PM2 supporting BP4 supporting

Variant details

Gene

MSH6

Transcript

NM_000179.3

Protein

NP_000170.1:p.(Arg178Leu)

gnomAD AF

1.239056037548354e-06 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

c.533G>T (p.Arg178Leu) is a missense variant in exon 3 of MSH6.

2

The variant is extremely rare in population databases (gnomAD v4.1 allele frequency = 1.24e-6; 2/1,614,132 alleles, 0 homozygotes), meeting PM2_Supporting per the InSiGHT MSH6 VCEP threshold of <0.00002.

3

Multiple lines of computational evidence support a benign effect: HCI prior probability for pathogenicity = 0.0003 (meeting BP4_Supporting threshold <0.11), REVEL score = 0.084, BayesDel score = -0.372, and SpliceAI max delta = 0.00.

4

In ClinVar (Variation ID 483842), the variant is classified as Uncertain Significance by the majority of clinical laboratories (3 VUS, 1 Likely Benign, 1 Benign), with review status 'criteria provided, single submitter' and no expert panel review.

5

No variant-specific functional studies (PS3/BS3), segregation data (PP1/BS4), tumor phenotype data (PP4/BP5), de novo observations (PS2), or pathogenic comparator variants at the same residue (PM5/PS1) were identified.

6

Applying the InSiGHT MSH6 VCEP v2.0.0 combining rules: one pathogenic supporting criterion (PM2_Supporting) and one benign supporting criterion (BP4_Supporting) yields conflicting evidence, classifying this variant as Uncertain Significance (Rule 31: >=1 Benign Supporting AND >=1 Pathogenic Supporting).

Final determination: Rule31 in the 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 is satisfied by the adjudicated criteria, so the variant is classified as Uncertain Significance - Conflicting Evidence.

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	N/A	PVS1 is not applicable to missense variants. c.533G>T (p.Arg178Leu) is a missense substitution that does not introduce a premature termination codon, affect a canonical splice site, or involve the initiation codon. The MSH6 VCEP PVS1 Decision Tree does not apply to missense variants.	pvs1_variant_assessment pvs1_gene_context
PS1	Not met	No alternative nucleotide change encoding p.Arg178Leu has been previously classified as Pathogenic or Likely Pathogenic by the InSiGHT VCEP. The variant is absent from the VCEP pilot variants spreadsheet and no ClinVar expert panel submissions exist for this residue.	clinvar vcep_vcep_pilot_variants_mmr
PS2	Not met	No de novo observations are documented for this variant. No publications or curated databases report de novo occurrence of c.533G>T (p.Arg178Leu) with confirmed maternity and paternity.	clinvar
PS3	Not met	No variant-specific calibrated functional assay data are available for p.Arg178Leu. The InSiGHT MMR functional assay SVI documentation does not include this variant. OncoKB reports 'Unknown Oncogenic Effect' with no curated functional evidence.	oncokb vcep_functional_assay_svi_documentation_mmr
PS4	N/A	PS4 is designated as Not Applicable by the MSH6 VCEP (InSiGHT Hereditary Colorectal Cancer/Polyposis EP Specifications v2.0.0). Case-control study data are not used for MSH6 variant classification under this framework.	cspec
PS5	Not met	PS5 is not defined in the MSH6 VCEP criteria set (the companion criterion BP6 is explicitly Not Applicable per VCEP). No reputable source has reported this variant as Pathogenic. The aggregate ClinVar classification is Uncertain Significance (3 clinical laboratories VUS, 1 LB, 1 B).	clinvar cspec
PM1	N/A	PM1 is designated as Not Applicable by the MSH6 VCEP. The InSiGHT EP does not apply the mutational hotspot criterion for MSH6 variant classification.	cspec
PM2	Met	The variant is extremely rare in gnomAD v4.1 with an allele frequency of 1.24e-6 (2/1,614,132 alleles), which is below the VCEP PM2_Supporting threshold of <0.00002 (<1 in 50,000 alleles). Absent in gnomAD-Canada.	gnomad_v4 gnomad_canada
PM5	Not met	No different missense variant at amino acid residue Arg178 has been classified as Pathogenic or Likely Pathogenic by the InSiGHT VCEP. The PM5 candidates search returned zero same-residue comparator variants. Without a pathogenic comparator at this residue, PM5 cannot be applied.	pm5_candidates clinvar
PM6	N/A	PM6 is designated as Not Applicable by the MSH6 VCEP. De novo evidence is adjudicated under PS2 in this framework.	cspec
PP1	Not met	No co-segregation data are available for c.533G>T (p.Arg178Leu). No published pedigrees or Bayes likelihood ratio analyses have been performed for this variant.
PP2	N/A	PP2 is designated as Not Applicable by the MSH6 VCEP. The criterion for low rate of benign missense variation does not apply per the InSiGHT EP specifications.	cspec
PP3	Not met	The HCI prior probability for pathogenicity is 0.0003 for p.Arg178Leu in MSH6, which is well below the VCEP PP3_Supporting threshold (>0.68). SpliceAI delta score is 0.00, confirming no predicted splicing impact. REVEL score is 0.084 and BayesDel is -0.372, both consistent with a benign in silico profile.	hci_prior spliceai revel bayesdel
PP4	Not met	No tumor phenotype data are available for this variant. No reports of MSI-H tumors, MMR protein expression loss, or other LS-spectrum tumor characteristics in carriers of c.533G>T have been identified.
PP5	N/A	PP5 is designated as Not Applicable by the MSH6 VCEP. The InSiGHT EP does not use the 'reputable source' criterion for pathogenic classification.	cspec
BA1	Not met	The gnomAD v4.1 allele frequency is 1.24e-6 (0.000124%), which is far below the VCEP BA1 stand-alone threshold of >=0.0022 (0.22%). The variant is not a founder pathogenic variant.	gnomad_v4
BS1	Not met	The gnomAD v4.1 allele frequency is 1.24e-6 (0.000124%), which is below the VCEP BS1_Strong threshold range of >=0.00022 (0.022%) to <0.0022 (0.22%). The highest subpopulation frequency (Middle Eastern, AF = 0.000165) also falls below this threshold.	gnomad_v4
BS2	Not met	No evidence of co-occurrence in trans with a known pathogenic MSH6 variant has been reported. No individual with biallelic MSH6 variants has been identified with CRC after age 45 and absence of CMMRD features.
BS3	Not met	No variant-specific functional studies demonstrating benign effect are available for p.Arg178Leu. The InSiGHT MMR functional assay SVI documentation does not include this variant, and no calibrated functional odds for pathogenicity can be calculated.	vcep_functional_assay_svi_documentation_mmr
BS4	Not met	No segregation data are available to assess lack of co-segregation with disease. No pedigree analysis with Bayes likelihood ratio has been performed for this variant.
BP1	N/A	BP1 is designated as Not Applicable by the MSH6 VCEP. The criterion for missense variants in genes where only LOF causes disease does not apply per the InSiGHT EP specifications.	cspec
BP2	N/A	BP2 is designated as Not Applicable by the MSH6 VCEP.	cspec
BP3	N/A	In-frame insertions/deletions in repetitive regions without known function are not applicable to this missense substitution variant.
BP4	Met	The HCI prior probability for pathogenicity is 0.0003 for p.Arg178Leu in MSH6, which is well below the VCEP BP4_Supporting threshold of <0.11. This is further supported by a REVEL score of 0.084, BayesDel score of -0.372, and SpliceAI max delta score of 0.00, all consistent with a benign computational profile.	hci_prior revel bayesdel spliceai
BP5	Not met	No tumor data are available to apply BP5. No reports of MSS tumors, BRAF V600E mutations, or MLH1 methylation in tumors from carriers of this variant were identified.
BP6	N/A	BP6 is designated as Not Applicable by the MSH6 VCEP. The InSiGHT EP does not use the 'reputable source' criterion for benign classification.	cspec
BP7	N/A	BP7 is applicable only to synonymous (silent) or intronic variants at or beyond -21/+7 splice positions. c.533G>T is a missense variant (p.Arg178Leu) and does not meet BP7 criteria.

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