LYFE Sciences · Project HERA
Variant Interpretation · Classification Report
Generated: 2026-06-14
Case ID: NM_000179.3_c.260_21T_G_20260614_175157
Framework: ACMG/AMP 2015
Variant classification summary

NM_000179.3:c.260+21T>G

MSH6  · NP_000170.1:p.?  · NM_000179.3
GRCh37: chr2:48010653 T>G  ·  GRCh38: chr2:47783514 T>G
Gene: MSH6 Transcript: NM_000179.3
Final call
Likely Benign
PM2 supporting BP4 supporting benign BP7 supporting benign
All criteria require review: For research and educational purposes only.
Variant details
Gene
MSH6
Transcript
NM_000179.3
Protein
NP_000170.1:p.?
gnomAD AF
4.321676810602514e-06 (v4.1)
ClinVar
Likely benign
OncoKB
Classification rationale
Interpretation summary
Generated evidence synthesis
1
NM_000179.3:c.260+21T>G in MSH6 is an intronic variant located at position +21 of intron 1. SpliceAI predicts no splicing impact (max delta score = 0.00).
2
The variant is present at extremely low frequency in gnomAD v4.1 (6/1,388,350 alleles, AF = 4.32e-06, grpmax FAF = 1.10e-05), meeting the InSiGHT MSH6 VCEP v2.0.0 PM2_Supporting criterion (AF < 0.00002).
3
The variant is absent from gnomAD v2.1 (0/34,192 alleles).
4
SpliceAI predicts no splicing impact (max delta = 0.00), meeting the VCEP BP4_Supporting criterion (delta ≤ 0.1 for intronic variants).
5
The variant is intronic at position +21, meeting the VCEP BP7_Supporting criterion (intronic variant at or beyond +7 from the exon boundary).
6
The gnomAD v4.1 grpmax FAF (1.10e-05) does not meet VCEP BA1 (≥0.0022) or BS1 (≥0.00022) frequency thresholds.
7
This variant has been reported in ClinVar as Likely benign by one clinical laboratory (ClinVar Variation ID: 491905).
Final determination: Rule19 in the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH6 Version 2.0.0 v2.0.0 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 N/A This intronic variant at c.260+21 (intron 1, +21 position) does not qualify for PVS1 under the InSiGHT MSH6 VCEP v2.0.0: it is not a nonsense/frameshift variant introducing a PTC ≤ codon 1341, not a canonical splice site variant (±1, ±2), not a large genomic alteration, and no mRNA splicing aberration has been confirmed by patient RNA assays.
cspec pvs1_generic_framework
PS1 N/A PS1 under the InSiGHT MSH6 VCEP v2.0.0 applies only to missense variants encoding the same amino acid change as a known pathogenic variant, or variants affecting the same non-canonical splice nucleotide as a confirmed pathogenic splice variant. This intronic substitution at c.260+21 does not change an amino acid and no pathogenic variant has been established at this intronic position.
cspec
PS2 Not assessed No de novo observation data are available for NM_000179.3:c.260+21T>G. The InSiGHT MSH6 VCEP v2.0.0 requires de novo points (≥0.5) based on confirmed de novo occurrences; none have been identified in the evidence sources for this case.
PS3 Not assessed No calibrated functional assay data are available for NM_000179.3:c.260+21T>G. The InSiGHT MSH6 VCEP v2.0.0 requires functional odds for pathogenicity from calibrated assays or MMR functional defect data per the functional assay flowchart. The variant was not found in the VCEP functional assay documentation spreadsheet, and no functional evidence was identified in the literature or OncoKB.
PS4 N/A PS4 is declared Not Applicable by the InSiGHT MSH6 VCEP v2.0.0 and is not used in this framework.
cspec
PS5 N/A PS5 is not defined in the InSiGHT MSH6 VCEP v2.0.0 criteria set and is not used in this framework.
cspec
PM1 N/A PM1 is declared Not Applicable by the InSiGHT MSH6 VCEP v2.0.0 as no mutational hotspot or critical functional domain criteria are specified for this gene.
cspec
PM2 Met NM_000179.3:c.260+21T>G has an allele frequency of 4.32e-06 (6/1,388,350 alleles, grpmax FAF = 1.10e-05) in gnomAD v4.1, which is below the InSiGHT MSH6 VCEP v2.0.0 PM2_Supporting threshold of <0.00002 (1 in 50,000 alleles).
gnomad_v4 cspec
PM5 N/A PM5 applies only to missense changes at an amino acid residue where a different missense change has been classified as pathogenic/likely pathogenic. This variant is an intronic substitution and does not alter an amino acid residue.
cspec pm5_candidates
PM6 N/A PM6 is declared Not Applicable by the InSiGHT MSH6 VCEP v2.0.0; de novo evidence is assessed under PS2 instead.
cspec
PP1 Not assessed No co-segregation data are available for NM_000179.3:c.260+21T>G. The InSiGHT MSH6 VCEP v2.0.0 requires Bayes likelihood ratios from pedigree analysis (≥2.08 for supporting, ≥4.3 for moderate, ≥18.7 for strong). No pedigree or segregation studies were identified in the literature or ClinVar submissions.
PP2 N/A PP2 is declared Not Applicable by the InSiGHT MSH6 VCEP v2.0.0; missense variants in a gene with low rate of benign missense changes does not apply.
cspec
PP3 Not met Under the InSiGHT MSH6 VCEP v2.0.0, PP3 applies to (a) missense variants with HCI prior >0.68, or (b) intronic/splice variants with SpliceAI delta score ≥ 0.2. This is an intronic variant and SpliceAI predicts no splicing impact (max delta score = 0.00), falling below the 0.2 threshold. The variant is not missense and has no HCI prior score.
cspec spliceai
PP4 Not assessed No tumor phenotype data (MSI status, MMR IHC) are available for carriers of NM_000179.3:c.260+21T>G. The InSiGHT MSH6 VCEP v2.0.0 requires MSI-H tumors and/or loss of MMR protein expression consistent with the variant location.
PP5 N/A PP5 is declared Not Applicable by the InSiGHT MSH6 VCEP v2.0.0 and is not used in this framework.
cspec
BA1 Not met Under the InSiGHT MSH6 VCEP v2.0.0, BA1 requires gnomAD v4 grpmax filtering allele frequency ≥ 0.0022 (0.22%). The grpmax FAF for this variant is 1.10e-05 (0.0011%), far below the BA1 stand-alone threshold.
gnomad_v4 cspec
BS1 Not met Under the InSiGHT MSH6 VCEP v2.0.0, BS1 requires gnomAD v4 grpmax filtering allele frequency ≥ 0.00022 (0.022%) and < 0.0022. The grpmax FAF for this variant is 1.10e-05 (0.0011%), below the BS1 threshold.
gnomad_v4 cspec
BS2 Not assessed No data are available demonstrating co-occurrence in trans with a known pathogenic MSH6 variant in a patient with colorectal cancer after age 45 without CMMRD features. The InSiGHT MSH6 VCEP v2.0.0 requires confirmed phase and exclusion of CMMRD per the CMMRD diagnostic table.
BS3 Not assessed No calibrated functional assay data are available for NM_000179.3:c.260+21T>G. While SpliceAI predicts no splicing impact (delta = 0.00), the InSiGHT MSH6 VCEP v2.0.0 BS3 rule for intronic variants requires laboratory mRNA assays (with NMD inhibition) demonstrating no associated mRNA aberration. In silico prediction alone is insufficient to meet BS3.
cspec spliceai
BS4 Not assessed No co-segregation data are available for NM_000179.3:c.260+21T>G. The InSiGHT MSH6 VCEP v2.0.0 requires Bayes likelihood ratios from pedigree analysis demonstrating lack of co-segregation with disease.
BP1 N/A BP1 is declared Not Applicable by the InSiGHT MSH6 VCEP v2.0.0; this criterion (missense variant in a gene where primarily truncating variants cause disease) is not used for MSH6.
cspec
BP2 N/A BP2 is declared Not Applicable by the InSiGHT MSH6 VCEP v2.0.0 and is not used in this framework.
cspec
BP3 N/A BP3 is skipped per directive: this is a substitution variant, not an in-frame deletion/insertion in a repetitive region.
BP4 Met Under the InSiGHT MSH6 VCEP v2.0.0, BP4_Supporting is met for intronic variants when SpliceAI predicts no splicing impact with delta score ≤ 0.1. SpliceAI predicts no significant splice impact for NM_000179.3:c.260+21T>G (max delta score = 0.00).
cspec spliceai
BP5 Not assessed No tumor data are available for NM_000179.3:c.260+21T>G. The InSiGHT MSH6 VCEP v2.0.0 requires MSS tumors, absence of MMR protein expression loss, or BRAF V600E/MLH1 methylation data. None have been identified for this variant.
BP6 N/A BP6 is declared Not Applicable by the InSiGHT MSH6 VCEP v2.0.0; this criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.
cspec
BP7 Met Under the InSiGHT MSH6 VCEP v2.0.0, BP7_Supporting applies to intronic variants at or beyond -21/+7 from the exon boundary. NM_000179.3:c.260+21T>G is located at position +21 in intron 1, which is beyond the +7 threshold, satisfying the VCEP BP7 rule.
cspec
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