Variant classification summary

NM_000179.3:c.4002-28_4002-26dupCTT

MSH6 · NP_000170.1:p.? · NM_000179.3

GRCh37: chr2:48033889 A>ACTT · GRCh38: chr2:47806750 A>ACTT

Gene: MSH6 Transcript: NM_000179.3

Final call

Benign

BA1 stand-alone benign BP4 supporting benign BP7 supporting benign

Variant details

Gene

MSH6

Transcript

NM_000179.3

Protein

NP_000170.1:p.?

gnomAD AF

0.0013415464760715985 (v4.1)

ClinVar

Benign

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

BA1 is met at stand-alone strength: gnomAD v4.1 grpmax filtering allele frequency is 0.027 (2.70%), far exceeding the VCEP threshold of ≥0.0022 (0.22%). The variant is observed in 6 homozygotes in v4.1 and 2 homozygotes in v2.1, and is not a known founder pathogenic variant.

2

BP7 is met at supporting benign strength: the variant is an intronic duplication at positions -26 to -28 relative to exon 10, which is beyond the VCEP BP7 threshold of -21.

3

BP4 is met at supporting benign strength: SpliceAI predicts no splicing impact (max delta score = 0.00), meeting the VCEP BP4_Supporting threshold of ≤0.1 for intronic variants.

4

Per the InSiGHT MSH6 VCEP v2.0.0 combination rules, BA1 stand-alone alone is sufficient for a Benign classification (Rule 17).

Final determination: Rule17 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 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	Intronic duplication at c.4002-28_4002-26 (26-28 nucleotides upstream of exon 10 in MSH6 intron 9). Does not affect a canonical splice donor/acceptor site and is not predicted to alter splicing (SpliceAI max delta = 0.00). Does not fall into any VCEP PVS1 strength category (nonsense/frameshift, large genomic alteration, IVS±1,2, or patient mRNA-confirmed splicing aberration).	spliceai
PS1	N/A	Variant is an intronic duplication, not a missense substitution and not affecting a non-canonical splice nucleotide with a known pathogenic comparator.
PS2	Not met	No de novo observations have been reported for this variant in any database or literature.
PS3	Not met	No calibrated functional assay data available for this variant. No patient mRNA or minigene splicing assay demonstrating a damaging effect has been reported. The functional assay SVI documentation spreadsheet does not list this variant.
PS4	N/A	PS4 is designated as Not Applicable by the InSiGHT MSH6 VCEP v2.0.0; tumor IHC data (PP4) is used instead of proband counting.	cspec
PS5	N/A	PS5 is not a defined criterion in the InSiGHT MSH6 VCEP v2.0.0 framework.
PM1	N/A	PM1 is designated as Not Applicable by the InSiGHT MSH6 VCEP v2.0.0; there are no recognized mutational hot spots for MMR gene classification.	cspec
PM2	Not met	Variant is present in gnomAD v4.1 at an allele frequency of 0.134% (1883/1403604 alleles, 6 homozygotes), far exceeding the VCEP PM2_Supporting threshold of <0.002% (<1 in 50,000 alleles).	gnomad_v4 gnomad_v2
PM4	N/A	PM4 is designated as Not Applicable by the InSiGHT MSH6 VCEP v2.0.0; protein length changes from in-frame variants are not used due to lack of evidence.	cspec
PM5	N/A	Variant is an intronic duplication, not a missense change at an amino acid residue. PM5 requires a missense change at a residue where a different pathogenic missense has been established.
PM6	N/A	PM6 is designated as Not Applicable by the InSiGHT MSH6 VCEP v2.0.0.	cspec
PP1	Not met	No co-segregation data available for this variant. No pedigrees with formal Bayes likelihood ratio analysis have been reported.
PP2	N/A	PP2 is designated as Not Applicable by the InSiGHT MSH6 VCEP v2.0.0; missense variant in a gene with low rate of benign missense changes does not apply.	cspec
PP3	Not met	SpliceAI predicts no splicing impact (max delta score = 0.00), below the VCEP PP3_Supporting threshold of ≥0.2 for non-canonical splice variants. HCI prior is not applicable for this non-missense variant. No computational evidence supports a deleterious effect.	spliceai
PP4	Not met	No tumor phenotype data (MSI status, IHC for MMR protein expression) have been reported for patients carrying this variant.
PP5	N/A	PP5 is designated as Not Applicable for this VCEP by the InSiGHT MSH6 VCEP v2.0.0.	cspec
BA1	Met	gnomAD v4.1 grpmax filtering allele frequency is 0.027 (2.70%), far exceeding the VCEP BA1 stand-alone threshold of ≥0.0022 (0.22%). The variant is observed in 6 homozygotes in v4.1 and 2 homozygotes in v2.1. Highest frequency in the East Asian population (2.83% in v4, 3.14% in v2). No evidence this is a founder pathogenic variant.	gnomad_v4 gnomad_v2 cspec
BS1	Not met	gnomAD v4.1 grpmax FAF is 0.027 (2.70%), which exceeds the VCEP BS1 upper bound of <0.0022 (0.22%). The variant frequency is too high for BS1 and is captured by BA1 instead.	gnomad_v4 cspec
BS2	Not met	No data demonstrating co-occurrence in trans with a known pathogenic MSH6 variant in a patient with colorectal cancer after age 45 without CMMRD features.
BS3	Not met	No laboratory functional assay data available demonstrating no splicing aberration or proficient MMR function. The VCEP BS3 rule for intronic variants requires mRNA aberration assessment by laboratory assays conducted with NMD inhibition; in silico SpliceAI prediction alone is insufficient. This variant is not listed in the VCEP calibrated functional assay documentation.	spliceai
BS4	Not met	No segregation data available to evaluate lack of co-segregation with disease.
BP1	N/A	BP1 is designated as Not Applicable by the InSiGHT MSH6 VCEP v2.0.0; missense variant in a gene where only LOF causes disease is not applicable.	cspec
BP2	N/A	BP2 is designated as Not Applicable by the InSiGHT MSH6 VCEP v2.0.0; BS2 is used instead.	cspec
BP3	N/A	BP3 is designated as Not Applicable by the InSiGHT MSH6 VCEP v2.0.0; in-frame deletions/insertions in a repetitive region without a known function is not used.	cspec
BP4	Met	SpliceAI predicts no splicing impact for this intronic variant (max delta score = 0.00), meeting the VCEP BP4_Supporting threshold of ≤0.1 per Walker et al. 2023.	spliceai cspec
BP5	Not met	No tumor phenotype data (MSS status, MMR IHC, BRAF V600E, MLH1 methylation) available for patients carrying this variant.
BP6	N/A	BP6 is designated as Not Applicable for this VCEP by the InSiGHT MSH6 VCEP v2.0.0.	cspec
BP7	Met	Intronic duplication located at positions -26 and -28 relative to exon 10, which is at or beyond the VCEP BP7 threshold of -21. SpliceAI predicts no splicing impact (max delta = 0.00).	spliceai cspec

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