Variant classification summary

NM_000179.3:c.4001+32_4001+35dupAACT

MSH6 · NP_000170.1:p.? · NM_000179.3

GRCh37: chr2:48033816 A>ATAAC · GRCh38: chr2:47806677 A>ATAAC

Gene: MSH6 Transcript: NM_000179.3

Final call

Likely Benign

BP4 supporting BP7 supporting

Variant details

Gene

MSH6

Transcript

NM_000179.3

Protein

NP_000170.1:p.?

gnomAD AF

9.956155346079716e-05 (v4.1)

ClinVar

Likely benign

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000179.3:c.4001+32_4001+35dup is an intronic duplication in MSH6 intron 9, located 32 bases downstream of exon 9.

2

This variant is observed in gnomAD v4.1 at an allele frequency of 0.00996% (159/1,597,002 alleles, 0 homozygotes) with a grpmax filtering allele frequency of 0.0203%.

3

SpliceAI predicts no splicing impact (max delta score = 0.00), meeting VCEP BP4_Supporting for intronic variants.

4

The variant is intronic at position c.4001+32, beyond the +7 boundary, satisfying VCEP BP7_Supporting.

5

This variant has been reported in ClinVar as Likely benign by 4 clinical laboratories and Benign by 1 clinical laboratory (VariationID 89502, 1-star review status).

6

No pathogenic criteria are met. VCEP PVS1 is not applicable as the variant is a deep intronic duplication without evidence of a splicing aberration. No variant-specific functional, segregation, or tumor phenotype data are available.

7

Applying the InSiGHT MSH6 VCEP v2.0 combination rules: BP4_Supporting + BP7_Supporting (≥2 benign supporting criteria) classifies this variant as Likely Benign (Rule 19).

Final determination: Rule19 in the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH6 Version 2.0 v2.0 criteria-combination framework is satisfied by the adjudicated criteria, so the variant is classified as Likely Benign.

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	Not met	NM_000179.3:c.4001+32_4001+35dup is an intronic duplication located 32 bases downstream of exon 9. Under the InSiGHT MSH6 VCEP v2.0, PVS1 applies only to nonsense/frameshift variants introducing a PTC ≤ codon 1360, large genomic alterations, IVS±1/±2 splice site variants, initiation codon variants, tandem duplications of ≥1 exon, or mRNA-confirmed splicing aberrations. This intronic variant does not fall into any PVS1 strength bucket.	cspec pvs1_gene_context pvs1_variant_assessment
PS1	Not met	VCEP PS1 requires either a same-amino-acid missense change with a different nucleotide, or a variant affecting the same non-canonical splice nucleotide as a known pathogenic splice variant with similar or worse SpliceAI prediction. This intronic duplication is not a missense, and the duplicated bases (c.4001+32 to +35) are not at a splice consensus nucleotide. No known pathogenic splice variant at this position exists.	cspec
PS2	Not met	No de novo observation data is available for this variant. None of the reviewed publications or ClinVar submissions report de novo occurrence.
PS3	Not met	No variant-specific functional data exists for NM_000179.3:c.4001+32_4001+35dup. The InSiGHT MSH6 VCEP PS3 requires calibrated functional assay odds ratios or MMR functional defects per the functional assay flowchart. This intronic variant has not been functionally tested. SpliceAI predicts no splicing impact (delta = 0.00), but this alone does not constitute functional evidence of pathogenicity.	spliceai
PS4	N/A	PS4 is designated as not applicable by the InSiGHT MSH6 VCEP v2.0.	cspec
PS5	Not met	No novel missense variant at the same amino acid position has been reported as pathogenic. This variant is an intronic duplication and does not produce a protein-level change amenable to PS5 assessment.
PM1	N/A	PM1 is designated as not applicable by the InSiGHT MSH6 VCEP v2.0.	cspec
PM2	Not met	VCEP PM2_Supporting requires absent/extremely rare allele frequency <0.00002 (<1 in 50,000 alleles) in gnomAD v4. This variant is present in gnomAD v4.1 at AF=9.96e-05 (159/1,597,002 alleles), approximately 5-fold above the VCEP threshold. The variant is observed across multiple populations including South Asian (AF=0.00021), Remaining individuals (AF=0.00037), and European (non-Finnish).	gnomad_v4 cspec
PM4	N/A	PM4 is designated as not applicable by the InSiGHT MSH6 VCEP v2.0.	cspec
PM5	N/A	PM5 requires a missense change at an amino acid residue where a different missense change was classified as Pathogenic/Likely Pathogenic by the VCEP. This variant is an intronic duplication (c.4001+32_4001+35dup) with no protein-level consequence (NP_000170.1:p.?), and is not eligible for classic same-residue missense PM5 assessment.	pm5_candidates cspec
PM6	N/A	PM6 is designated as not applicable by the InSiGHT MSH6 VCEP v2.0.	cspec
PP1	Not met	No co-segregation data is available for this variant. VCEP PP1 requires combined Bayes Likelihood Ratio from pedigree analysis; no such data is present in ClinVar submissions or the available literature.
PP2	N/A	PP2 is designated as not applicable by the InSiGHT MSH6 VCEP v2.0 (missense variant in a gene with low rate of benign missense changes does not apply).	cspec
PP3	Not met	VCEP PP3 for non-canonical splice variants requires SpliceAI delta ≥ 0.2. SpliceAI predicts no splicing impact for this variant (max delta score = 0.00). For missense variants, VCEP PP3 requires HCI prior >0.68, but this is an intronic duplication and HCI priors are not applicable. PP3 is not met.	spliceai cspec
PP4	Not met	No tumor phenotype data (MSI status, IHC, or MMR protein expression) is available for patients carrying this variant. VCEP PP4 requires MSI-H tumors and/or loss of MMR protein expression consistent with the variant location.
PP5	N/A	PP5 is designated as not applicable by the InSiGHT MSH6 VCEP v2.0. Additionally, the ClinVar entry for this variant (VariationID 89502) has only 1-star review status (criteria provided, single submitter), which does not meet the 3-star expert panel threshold required for the PP5 global override rule.	cspec clinvar
BA1	Not met	VCEP BA1 Stand-Alone requires gnomAD v4 grpmax filtering allele frequency ≥ 0.0022 (0.22%). This variant has gnomAD v4 grpmax FAF = 0.00020269 (0.0203%), which is approximately 10-fold below the BA1 threshold.	gnomad_v4 cspec
BS1	Not met	VCEP BS1_Strong requires gnomAD v4 grpmax filtering allele frequency ≥ 0.00022 (0.022%) and < 0.0022. This variant has gnomAD v4 grpmax FAF = 0.00020269 (0.0203%), which falls just below the 0.00022 threshold. BS1 is not met.	gnomad_v4 cspec
BS2	Not met	No evidence of co-occurrence in trans with a known pathogenic MSH6 variant in a patient with colorectal cancer after age 45 without clinical manifestations of CMMRD. VCEP BS2 requires confirmed phase via parental testing.
BS3	Not met	VCEP BS3_Strong for intronic variants requires laboratory assays with NMD inhibition demonstrating no associated mRNA aberration. While SpliceAI predicts no splicing impact (delta = 0.00), this is an in silico prediction and does not satisfy the VCEP requirement for laboratory-based functional evidence. No calibrated functional assay data or mRNA studies exist for this variant.	spliceai cspec
BS4	Not met	No co-segregation data is available to assess lack of segregation with disease. VCEP BS4 requires combined Bayes Likelihood Ratio from pedigree analysis showing lack of co-segregation.
BP1	N/A	BP1 is designated as not applicable by the InSiGHT MSH6 VCEP v2.0 (missense variant in a gene where only loss of function causes disease is not applicable).	cspec
BP2	N/A	BP2 is designated as not applicable by the InSiGHT MSH6 VCEP v2.0.	cspec
BP3	N/A	BP3 is designated as not applicable by the InSiGHT MSH6 VCEP v2.0 (in-frame deletions/insertions in a repetitive region without a known function is not used).	cspec
BP4	Met	VCEP BP4_Supporting for intronic variants: SpliceAI predicts no splicing impact with delta score ≤ 0.1 as per Walker et al 2023. This intronic duplication at c.4001+32_4001+35 has a SpliceAI max delta score of 0.00, indicating no predicted effect on splicing. The variant also satisfies BP7; BP4 and BP7 may both be applied per VCEP rules.	spliceai cspec
BP5	Not met	No tumor data (MSS/MSI status, IHC for MMR proteins, BRAF V600E, or MLH1 methylation) is available. VCEP BP5 requires observations of tumors with MSS and/or no loss of MMR protein expression, or BRAF V600E/MLH1 methylation with MSI-H/MLH1 loss.
BP6	N/A	BP6 is designated as not applicable by the InSiGHT MSH6 VCEP v2.0. Additionally, the ClinVar entry for this variant (VariationID 89502) has only 1-star review status, which does not meet the 3-star expert panel threshold required for the BP6 global override rule.	cspec clinvar
BP7	Met	VCEP BP7_Supporting: synonymous or intronic variant at or beyond -21/+7 (5′/3′ exonic). NM_000179.3:c.4001+32_4001+35dup is an intronic variant located 32 bases downstream of exon 9, well beyond the +7 boundary. This criterion may be applied alongside BP4 per VCEP rules.	cspec

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