Variant classification summary

NM_000179.3:c.2526T>G

MSH6 · NP_000170.1:p.(Ala842=) · NM_000179.3

GRCh37: chr2:48027648 T>G · GRCh38: chr2:47800509 T>G

Gene: MSH6 Transcript: NM_000179.3

Final call

Likely Benign

PM2 supporting BP4 supporting BP7 supporting

Variant details

Gene

MSH6

Transcript

NM_000179.3

Protein

NP_000170.1:p.(Ala842=)

gnomAD AF

8.059486449523436e-06 (v4.1)

ClinVar

Likely benign

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

c.2526T>G (p.Ala842=) is a synonymous variant in MSH6 exon 4 with no predicted effect on splicing (SpliceAI max delta = 0.00).

2

The variant is extremely rare in population databases, with an overall allele frequency of 8.06×10⁻⁶ in gnomAD v4.1 (13/1,613,006 alleles, 0 homozygotes), meeting PM2_Supporting per VCEP MSH6 (threshold <0.00002).

3

As a synonymous variant with no predicted splicing impact (SpliceAI delta = 0.00), BP4_Supporting is met per VCEP MSH6 rule for synonymous variants with SpliceAI delta ≤0.1.

4

The variant is a synonymous substitution located deep within exon 4 (c.628-3172), far from splice junctions, meeting BP7_Supporting per VCEP MSH6 rule for synonymous variants at or beyond -21/+7 position.

5

This variant has been reported in ClinVar as Likely benign by 5 clinical laboratories, Likely Benign by 1, and Benign by 1 (ClinVar ID: 186376, review status: criteria provided, single submitter). However, BP6 is not applicable per VCEP rules.

6

No functional studies, segregation data, tumor phenotype data, or de novo observations have been reported for this variant. No publications mention NM_000179.3:c.2526T>G specifically.

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	PVS1 is not applicable to synonymous variants. The VCEP MSH6 PVS1 rules are limited to nonsense, frameshift, canonical splice site, and initiation codon variants. c.2526T>G (p.Ala842=) is a synonymous substitution with no predicted effect on splicing (SpliceAI max delta = 0.00).	spliceai
PS1	N/A	PS1 is not applicable to synonymous variants. The VCEP MSH6 PS1 rules require a missense substitution encoding the same amino acid change as a known pathogenic/likely pathogenic variant, or a variant affecting the same non-canonical splice nucleotide as a known pathogenic splice variant. c.2526T>G is synonymous and does not alter the amino acid.
PS2	Not met	No de novo observations have been reported for this variant. VCEP MSH6 PS2 requires de novo points from confirmed parentage testing; no such data are available.
PS3	Not met	No variant-specific functional data are available for c.2526T>G. OncoKB reports no curated functional evidence. The VCEP functional assay documentation does not include this variant. No calibrated functional odds for pathogenicity can be assessed.	oncokb
PS4	N/A	PS4 is explicitly designated as Not Applicable by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP for MSH6.	cspec
PS5	N/A	PS5 is not included in the VCEP MSH6 criteria; PP5 is also explicitly designated as Not Applicable by this VCEP. PS5 is not assessed under this framework.	cspec
PM1	N/A	PM1 is explicitly designated as Not Applicable by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP for MSH6.	cspec
PM2	Met	c.2526T>G is extremely rare in population databases. In gnomAD v4.1 the overall allele frequency is 8.06×10⁻⁶ (13/1,613,006 alleles, 0 homozygotes), which is below the VCEP MSH6 PM2_Supporting threshold of <0.00002 (<1 in 50,000 alleles). The variant is also rare in gnomAD v2.1 (AF=3.62×10⁻⁵, 9/248,608 alleles).	gnomad_v4 gnomad_v2 cspec
PM5	N/A	PM5 requires a missense change at an amino acid residue where a different pathogenic/likely pathogenic missense variant has been established. c.2526T>G is a synonymous variant (p.Ala842=) and does not alter the amino acid; no missense comparator analysis can be performed. The pm5_candidates artifact confirms ineligibility.	pm5_candidates
PM6	N/A	PM6 is explicitly designated as Not Applicable by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP for MSH6.	cspec
PP1	Not met	No co-segregation data are available for this variant. VCEP MSH6 PP1 requires co-segregation with disease in pedigrees with a combined Bayes Likelihood Ratio exceeding defined thresholds; no such data have been reported.
PP2	N/A	PP2 is explicitly designated as Not Applicable by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP for MSH6.	cspec
PP3	Not met	VCEP MSH6 PP3 criteria do not apply to this variant. The HCI prior lookup for c.2526T>G returned no result (variant not in the MSH6 HCI priors table). The SpliceAI-based PP3 rule (delta score ≥0.2 for non-canonical splice nucleotides) does not apply because SpliceAI max delta is 0.00 and this is an exonic synonymous variant, not a splice region variant.	spliceai
PP4	Not met	No MSI-H tumor data or MMR protein expression data are available for this variant. VCEP MSH6 PP4 requires MSI-H colorectal/endometrial tumors and/or loss of MMR protein expression consistent with the variant location. No such clinical tumor data have been identified.
PP5	N/A	PP5 is explicitly designated as Not Applicable by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP for MSH6.	cspec
BA1	Not met	The gnomAD v4 grpmax filtering allele frequency for c.2526T>G is 0.0001539 (0.015%), which is far below the VCEP MSH6 BA1 stand-alone threshold of ≥0.0022 (0.22%). The variant does not meet the BA1 frequency criterion.	gnomad_v4 cspec
BS1	Not met	The gnomAD v4 grpmax filtering allele frequency for c.2526T>G is 0.0001539 (0.015%), which falls below the VCEP MSH6 BS1 threshold of ≥0.00022 (0.022%). The variant is too rare in population databases to qualify for BS1.	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 has been identified. VCEP BS2 requires confirmed-phase trans co-occurrence with a pathogenic variant in an individual without CMMRD features.
BS3	Not met	No variant-specific functional data demonstrating benign impact are available for c.2526T>G. VCEP MSH6 BS3 requires calibrated functional assays with functional odds for pathogenicity ≤0.05, or synonymous/intronic variants with no mRNA aberration. While the variant is synonymous, no laboratory mRNA assays confirming normal splicing have been performed.
BS4	Not met	No segregation data demonstrating lack of co-segregation with disease are available for this variant. VCEP BS4 requires pedigrees with a combined Bayes Likelihood Ratio meeting defined thresholds.
BP1	N/A	BP1 is explicitly designated as Not Applicable by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP for MSH6.	cspec
BP2	N/A	BP2 is explicitly designated as Not Applicable by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP for MSH6.	cspec
BP4	Met	SpliceAI predicts no splicing impact for this synonymous variant (max delta score = 0.00, ≤0.1). Per the VCEP MSH6 BP4_Supporting rule, synonymous variants with SpliceAI delta score ≤0.1 meet BP4_Supporting.	spliceai cspec
BP5	Not met	No tumor data (MSS tumors, retained MMR protein expression, or BRAF V600E/MLH1 methylation) are available for this variant. VCEP MSH6 BP5 requires observation of MSS tumors without MMR loss or BRAF/MLH1 methylation evidence inconsistent with Lynch syndrome.
BP6	N/A	BP6 is explicitly designated as Not Applicable by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP for MSH6.	cspec
BP7	Met	c.2526T>G is a synonymous (silent) variant located at coding position 2526 in exon 4 (c.628-3172), well within the exon interior and far from canonical splice sites. Per VCEP MSH6 BP7, synonymous variants at or beyond the -21/+7 splice region meet BP7_Supporting. Variants may satisfy both BP7 and BP4 per VCEP rules.	cspec spliceai

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