Variant classification summary

NM_000179.3:c.4002-26_4002-25insCT

MSH6 · NP_000170.1:p.? · NM_000179.3

GRCh37: chr2:48033891 T>TTC · GRCh38: chr2:47806752 T>TTC

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

0.0018464837390302982 (v4.1)

ClinVar

Benign

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000179.3:c.4002-26_4002-25insCT is present in gnomAD v4.1 at a grpmax filtering allele frequency of 2.41% in the East Asian population, exceeding the InSiGHT MSH6 VCEP BA1 stand-alone benign threshold of 0.22%. This population frequency is incompatible with a pathogenic role in Lynch syndrome.

2

SpliceAI predicts no splicing impact (max delta = 0.02), meeting the VCEP BP4_Supporting criterion for intronic variants.

3

The variant is located at intronic positions -26/-25, satisfying the VCEP BP7_Supporting criterion for intronic variants at or beyond -21/+7.

4

No pathogenic evidence criteria are met: PVS1 is not applicable (deep intronic, no null-allele evidence); PM2 is not met (gnomAD v4.1 AF = 0.185%); PP3 is not met (SpliceAI delta 0.02 < 0.2); and no functional, segregation, de novo, or tumor phenotype data support pathogenicity.

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	NM_000179.3:c.4002-26_4002-25insCT is a deep intronic 2-bp insertion in intron 9, 26-25 nucleotides upstream of exon 10. It does not introduce a premature termination codon, is not located at a canonical ±1,2 splice site, and no RNA-based evidence of a splicing aberration leading to a null allele is available. The variant does not meet any of the VCEP PVS1 strength rules for MSH6.	spliceai pvs1_generic_framework
PS1	Not met	PS1 requires either the same amino acid change as a known pathogenic missense variant, or a variant at the same non-canonical splice nucleotide as a confirmed pathogenic splice variant with similar or worse SpliceAI prediction. This intronic insertion does not encode an amino acid change, and no pathogenic variant has been established at the c.4002-26/-25 position.	cspec
PS2	Not met	No de novo observations of NM_000179.3:c.4002-26_4002-25insCT have been reported in ClinVar, the published literature, or public databases. The VCEP PS2 point-based system cannot be applied.
PS3	Not met	No functional studies (MMR activity assays, protein expression, or splicing reporter assays) directly testing NM_000179.3:c.4002-26_4002-25insCT were identified. The VCEP PS3 rules require calibrated functional assay odds for pathogenicity or MMR function defect evidence, none of which is available for this variant.
PS4	N/A	The InSiGHT MSH6 VCEP v2.0.0 declares PS4 Not Applicable for this gene.	cspec
PS5	N/A	PS5 is not included in the InSiGHT MSH6 VCEP v2.0.0 criteria set and is not applicable under this framework.	cspec
PM1	N/A	The InSiGHT MSH6 VCEP v2.0.0 declares PM1 Not Applicable for this gene.	cspec
PM2	Not met	The VCEP PM2 (Supporting) threshold requires absent or extremely rare allele frequency (<0.00002; <1 in 50,000 alleles) in gnomAD v4. NM_000179.3:c.4002-26_4002-25insCT is present in gnomAD v4.1 at an allele frequency of 0.00185 (186/100,732 alleles, ~9.3 per 50,000), which exceeds the PM2 threshold.	gnomad_v4
PM4	N/A	The InSiGHT MSH6 VCEP v2.0.0 declares PM4 Not Applicable for this gene.	cspec
PM5	N/A	PM5 applies only to missense variants at an amino acid residue where a different missense change has been classified as pathogenic. This is an intronic insertion and does not encode an amino acid change.	cspec
PM6	N/A	The InSiGHT MSH6 VCEP v2.0.0 declares PM6 Not Applicable for this gene.	cspec
PP1	Not met	No cosegregation data are available for NM_000179.3:c.4002-26_4002-25insCT. No pedigrees with combined Bayes likelihood ratio have been reported.
PP2	N/A	The InSiGHT MSH6 VCEP v2.0.0 declares PP2 Not Applicable (missense variant in a gene with low rate of benign missense changes does not apply).	cspec
PP3	Not met	For intronic variants, the VCEP PP3_Supporting rule requires SpliceAI delta score ≥ 0.2 for a predicted splice defect at non-canonical nucleotides. SpliceAI predicts no splicing impact (max delta = 0.02), which is well below the 0.2 threshold. The HCI prior is not applicable as this is not a missense substitution.	spliceai cspec
PP4	Not met	No tumor MSI or immunohistochemistry data are available for patients carrying NM_000179.3:c.4002-26_4002-25insCT. The VCEP PP4 rules require MSI-H colorectal/endometrial tumors and/or loss of MMR protein expression consistent with the variant location.
PP5	N/A	The InSiGHT MSH6 VCEP v2.0.0 declares PP5 Not Applicable for this gene.	cspec
BA1	Met	The grpmax filtering allele frequency in gnomAD v4.1 is 0.0241 (2.41%) in the East Asian population, which exceeds the VCEP BA1 threshold of ≥0.0022 (0.22%). The variant has a total v4.1 allele frequency of 0.00185 (186/100,732 alleles) and is not known to be a founder pathogenic variant. This frequency is incompatible with MSH6-associated Lynch syndrome prevalence.	gnomad_v4 cspec
BS1	Not met	The VCEP BS1 (Strong) threshold is grpmax FAF ≥ 0.00022 and < 0.0022 (0.022-0.22%). The observed grpmax FAF of 0.0241 (2.41%) exceeds the BS1 upper bound. This frequency range is instead captured by BA1 (Stand Alone).	gnomad_v4 cspec
BS2	Not met	BS2 requires co-occurrence in trans with a known pathogenic MSH6 variant in a patient with colorectal cancer after age 45 without CMMRD features. No such observation has been reported.
BS3	Not met	No calibrated functional assay data or laboratory-based mRNA splicing assays are available for NM_000179.3:c.4002-26_4002-25insCT. While SpliceAI predicts no splicing impact (delta 0.02), the VCEP BS3 rule requires laboratory assays conducted with nonsense-mediated decay inhibition, not in silico predictions alone.	spliceai
BS4	Not met	No pedigrees demonstrating lack of cosegregation with disease have been reported for this variant.
BP1	N/A	The InSiGHT MSH6 VCEP v2.0.0 declares BP1 Not Applicable (missense variant in a gene where only loss of function causes disease is not applicable).	cspec
BP2	N/A	The InSiGHT MSH6 VCEP v2.0.0 declares BP2 Not Applicable for this gene.	cspec
BP3	N/A	The InSiGHT MSH6 VCEP v2.0.0 declares BP3 Not Applicable (in-frame deletions/insertions in a repetitive region without a known function is not used).	cspec
BP4	Met	For intronic variants, the VCEP BP4_Supporting rule is met when SpliceAI predicts no splicing impact with a delta score ≤ 0.1. SpliceAI predicts no significant splice impact for this variant (max delta = 0.02).	spliceai cspec
BP5	Not met	BP5 requires MSS colorectal/endometrial tumors or BRAF V600E/MLH1 methylation with MSI-H/MLH1 loss. No tumor phenotype data are available for carriers of this variant.
BP6	N/A	The InSiGHT MSH6 VCEP v2.0.0 declares BP6 Not Applicable as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BP7	Met	NM_000179.3:c.4002-26_4002-25insCT is an intronic variant located at positions -26 and -25 relative to the exon 10 boundary, which is beyond -21 from the splice acceptor site. This satisfies the VCEP BP7 rule for intronic variants at or beyond -21/+7.	cspec

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.