Variant classification summary

NM_000179.3:c.3312del

MSH6 · NP_000170.1:p.(Phe1104LeufsTer11) · NM_000179.3

GRCh37: chr2:48030691 CT>C · GRCh38: chr2:47803552 CT>C

Gene: MSH6 Transcript: NM_000179.3

Final call

Pathogenic

PVS1 very strong PM2 supporting PP5 supporting

Variant details

Gene

MSH6

Transcript

NM_000179.3

Protein

NP_000170.1:p.(Phe1104LeufsTer11)

gnomAD AF

6.195587254933546e-07 (v4.1)

ClinVar

Pathogenic

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000179.3:c.3312del (p.Phe1104LeufsTer11) is a frameshift deletion in exon 5 of MSH6 predicted to introduce a premature termination codon at codon 1104, well within the VCEP threshold of codon 1341 for PVS1_VeryStrong.

2

This variant is extremely rare in population databases, with a single heterozygous observation in gnomAD v4.1 (AF = 6.20e-07; 1/1,614,052 alleles) and absent from gnomAD v2.1, meeting PM2_Supporting per MSH6 VCEP thresholds (AF <0.00002).

3

This variant has been classified as Pathogenic by the InSiGHT expert panel in ClinVar (Variation ID: 89371) and by six clinical laboratories. The ClinVar record cites PMIDs 16360201, 18269114, 20487569, and 27601186; however, full-text confirmation of variant-specific mention could not be verified for these papers, and PP5 is not applicable per VCEP guidance.

4

No de novo observations (PS2), calibrated functional assay data (PS3), segregation data (PP1/BS4), or tumor phenotype data (PP4/BP5) were identified in the literature for this specific variant.

5

Applying the MSH6 VCEP v2.0.0 combination rules: PVS1_VeryStrong alone meets Rule 1 (>=1 PVS1_VeryStrong), yielding a classification of Pathogenic.

Final determination: Rule4 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 Pathogenic.

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	Met	NM_000179.3:c.3312del is a frameshift deletion that introduces a premature termination codon at codon 1104 (p.Phe1104LeufsTer11). Per the ClinGen InSiGHT MSH6 VCEP v2.0.0, nonsense/frameshift variants introducing a PTC at or before codon 1341 qualify for PVS1_VeryStrong.	cspec
PS1	N/A	PS1 per the MSH6 VCEP applies to predicted missense substitutions encoding the same amino acid change as an established pathogenic variant, or variants affecting the same non-canonical splice nucleotide as a pathogenic splice variant. NM_000179.3:c.3312del is a frameshift deletion, not a missense or splice variant.
PS2	Not assessed	No de novo observation data were identified for NM_000179.3:c.3312del. The VCEP MSH6 PS2 criterion requires de novo points from confirmed de novo occurrences with parental testing. No published de novo reports or segregation data confirming de novo status for this variant were found in the literature or ClinVar submissions.
PS3	Not assessed	No calibrated functional assay data were identified for NM_000179.3:c.3312del in the VCEP MMR functional assay documentation spreadsheet. The VCEP PS3 criterion requires functional odds for pathogenicity from calibrated assays. OncoKB annotates this variant as Likely Oncogenic (Likely Loss-of-function) in a somatic context, but this does not constitute calibrated germline functional evidence per VCEP standards.
PS4	N/A	The MSH6 VCEP v2.0.0 explicitly marks PS4 as Not Applicable for this gene.	cspec
PS5	N/A	PS5 is not a criterion in the standard ACMG/AMP 2015 framework (PMID:25741868). The pathogenic criteria are PVS1, PS1-PS4, PM1-PM6, and PP1-PP5. The equivalent criterion for source-based pathogenicity evidence is PP5, which the MSH6 VCEP explicitly marks as Not Applicable.
PM1	N/A	The MSH6 VCEP v2.0.0 explicitly marks PM1 as Not Applicable for this gene.	cspec
PM2	Met	NM_000179.3:c.3312del is present in gnomAD v4.1 at an extremely low allele frequency (AF = 6.20e-07; 1/1,614,052 alleles; 0 homozygotes). Per the MSH6 VCEP v2.0.0, variants absent or with allele frequency <0.00002 (<1 in 50,000 alleles) in gnomAD v4 meet PM2_Supporting. The variant's AF (6.2e-07) is well below this threshold.	gnomad_v4
PM3	N/A	Trivially not applicable per user directive (skip instruction).
PM4	N/A	The MSH6 VCEP v2.0.0 explicitly marks PM4 as Not Applicable for this gene.	cspec
PM5	N/A	PM5 per the MSH6 VCEP applies to missense changes at an amino acid residue where a different missense change has been classified as Pathogenic/Likely Pathogenic. NM_000179.3:c.3312del is a frameshift deletion, not a missense variant. The pm5_candidates module confirmed the variant is not eligible for classic same-residue missense PM5 analysis.	pm5_candidates
PM6	N/A	The MSH6 VCEP v2.0.0 explicitly marks PM6 as Not Applicable for this gene.	cspec
PP1	Not assessed	No co-segregation data (Bayes Likelihood Ratio from pedigree analysis) were identified for NM_000179.3:c.3312del. The MSH6 VCEP requires formal segregation analysis using the COOL tool to compute combined Bayes LR thresholds (>2.08 for Supporting, >4.3 for Moderate, >18.7 for Strong). No pedigrees with this variant were available in the evidence.
PP2	N/A	The MSH6 VCEP v2.0.0 explicitly marks PP2 as Not Applicable for this gene.	cspec
PP3	N/A	PP3 per the MSH6 VCEP applies to missense variants (with HCI prior probability thresholds) or non-canonical splice variants (with SpliceAI delta score >=0.2). NM_000179.3:c.3312del is a frameshift deletion. Neither REVEL/BayesDel scores nor HCI prior probabilities are available for deletion variants. SpliceAI predicts no splice impact (max delta = 0.00). The VCEP also notes PVS1 should not be combined with PP3 for the same molecular evidence.	spliceai
PP4	Not assessed	No tumor phenotype data (MSI-H status, MMR IHC, or loss of protein expression) were identified for patients carrying NM_000179.3:c.3312del. The MSH6 VCEP PP4 criterion requires independent CRC/Endometrial MSI-H tumors and/or loss of MMR protein expression consistent with the variant location. No tumor-level evidence was found in the literature or ClinVar submissions for this specific variant.
PP5	Met	Expert panel International Society for Gastrointestinal Hereditary Tumours (InSiGHT) classified as Pathogenic.	cspec clinvar
BA1	Not met	The MSH6 VCEP BA1 criterion requires a gnomAD v4 Grpmax filtering allele frequency >=0.0022 (0.22%). NM_000179.3:c.3312del has an AF of 6.20e-07 in gnomAD v4.1 (1/1,614,052 alleles), far below the BA1 threshold. The variant is absent from gnomAD v2.1.	gnomad_v4
BS1	Not met	The MSH6 VCEP BS1 criterion requires a gnomAD v4 Grpmax filtering allele frequency >=0.00022 (0.022%). NM_000179.3:c.3312del has an AF of 6.20e-07 in gnomAD v4.1, which is well below the 0.022% threshold.	gnomad_v4
BS2	Not assessed	No evidence of co-occurrence in trans with a known pathogenic sequence variant in MSH6 was identified for this variant. The MSH6 VCEP BS2 criterion requires confirmed phase (parental testing) demonstrating in trans co-occurrence with a known pathogenic MSH6 variant in a patient with CRC after age 45 (or other LS cancer above median onset age) without CMMRD features.
BS3	Not assessed	No calibrated functional assay data supporting a benign effect were identified for NM_000179.3:c.3312del. The VCEP MMR functional assay documentation spreadsheet does not list this variant, and no literature was identified reporting functional evidence of normal MMR activity for this specific frameshift variant.
BS4	Not assessed	No co-segregation data were available to evaluate lack of co-segregation with disease. The MSH6 VCEP BS4 criterion requires a combined Bayes Likelihood Ratio <0.05 (Strong) or between 0.05-0.48 (Supporting) from formal pedigree analysis.
BP1	N/A	The MSH6 VCEP v2.0.0 explicitly marks BP1 as Not Applicable for this gene.	cspec
BP2	N/A	The MSH6 VCEP v2.0.0 explicitly marks BP2 as Not Applicable for this gene.	cspec
BP3	N/A	The MSH6 VCEP v2.0.0 explicitly marks BP3 as Not Applicable for this gene.	cspec
BP4	N/A	BP4 per the MSH6 VCEP applies to missense variants with HCI prior probability <0.11, or intronic/synonymous variants with SpliceAI delta <=0.1. NM_000179.3:c.3312del is a frameshift deletion and does not fall within either applicable category. SpliceAI predicts no splicing impact (max delta = 0.00), but the criterion does not apply to coding frameshift variants.	spliceai
BP5	Not assessed	No tumor phenotype data supporting a benign interpretation were identified for NM_000179.3:c.3312del. The MSH6 VCEP BP5 criterion requires CRC/Endometrial tumors with MSS and/or no loss of MMR protein expression, or BRAF V600E/MLH1 methylation with MSI-H/MLH1 loss. No such tumor-level data were available.
BP6	N/A	The MSH6 VCEP v2.0.0 explicitly marks BP6 as Not Applicable. The ClinGen SVI VCEP Review Committee recommends against using this criterion.	cspec
BP7	N/A	BP7 per the MSH6 VCEP applies to synonymous (silent) or intronic variants at or beyond -21/+7 (5'/3' exonic). NM_000179.3:c.3312del is a coding frameshift deletion in exon 5; it is neither synonymous nor intronic.

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.