Variant classification summary

NM_000179.3:c.643G>C

MSH6 · NP_000170.1:p.(Val215Leu) · NM_000179.3

GRCh37: chr2:48025765 G>C · GRCh38: chr2:47798626 G>C

Gene: MSH6 Transcript: NM_000179.3

Final call

PM2 supporting BP4 supporting benign

Variant details

Gene

MSH6

Transcript

NM_000179.3

Protein

NP_000170.1:p.(Val215Leu)

gnomAD AF

1.2416283210453517e-06 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000179.3:c.643G>C (p.Val215Leu) is a missense variant in exon 4 of MSH6. It is extremely rare in population databases (gnomAD v4.1 AF=1.24e-06), meeting PM2_Supporting per the InSiGHT MSH6 VCEP v2.0.0 threshold of <0.00002.

2

Multiple in silico predictors support a benign effect: the MSH6-specific HCI prior probability for pathogenicity is 0.0008, meeting BP4_Supporting (threshold <0.11). REVEL (0.139) and BayesDel (-0.503783) are also consistent with a benign prediction. SpliceAI predicts no splicing impact (max delta 0.09).

3

No variant-specific functional data, segregation data, tumor phenotype data, or de novo observations are available for this variant. The variant has not been classified by the VCEP pilot program and no comparator missense changes at codon 215 have been established as pathogenic.

4

This variant has been reported in ClinVar as Uncertain Significance by multiple clinical laboratories (ClinVar ID: 628619). Nine publications were reviewed; none mention NM_000179.3:c.643G>C.

Final determination: Rule31 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 Uncertain Significance - Conflicting Evidence.

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: NM_000179.3:c.643G>C is a missense variant (p.Val215Leu) and does not fall into any VCEP PVS1 null-variant bucket (nonsense, frameshift, canonical splice, large genomic alteration, or mRNA-confirmed splicing aberration).	pvs1_gene_context pvs1_variant_assessment
PS1	Not met	No nucleotide change encoding p.Val215Leu has been previously classified as Pathogenic or Likely Pathogenic by this VCEP. The VCEP pilot variants spreadsheet does not list any p.Val215 variant.	vcep_vcep_pilot_variants_mmr
PS2	Not met	No de novo observations are reported in ClinVar or the literature for NM_000179.3:c.643G>C. De novo scoring per VCEP PS2 point system cannot be applied.	clinvar
PS3	Not met	No variant-specific functional assay data for NM_000179.3:c.643G>C were identified in the VCEP functional assay documentation or in the reviewed literature. The HCI prior probability for pathogenicity is 0.0008, well below any calibrated functional odds threshold for PS3.	vcep_functional_assay_svi_documentation_mmr hci_prior
PS4	N/A	PS4 is designated Not Applicable by the InSiGHT MSH6 VCEP v2.0.0.	cspec
PS5	Not assessed	PS5 is not defined in the InSiGHT MSH6 VCEP v2.0.0 criteria set and is not addressed by any local custom gene framework. No assessment can be performed.	cspec
PM1	N/A	PM1 is designated Not Applicable by the InSiGHT MSH6 VCEP v2.0.0.	cspec
PM2	Met	NM_000179.3:c.643G>C is extremely rare in population databases. In gnomAD v4.1, the allele frequency is 1.24e-06 (2/1,610,788 alleles, no homozygotes), which is below the VCEP PM2 threshold of <0.00002 (<1 in 50,000 alleles).	gnomad_v4
PM5	Not met	No different missense change at codon 215 (Val215) has been classified as Pathogenic or Likely Pathogenic by this VCEP. PM5 candidate search returned no eligible comparators.	pm5_candidates vcep_vcep_pilot_variants_mmr
PM6	N/A	PM6 is designated Not Applicable by the InSiGHT MSH6 VCEP v2.0.0.	cspec
PP1	Not met	No co-segregation data are available for NM_000179.3:c.643G>C. No pedigrees with Bayes likelihood ratios are reported in ClinVar or the reviewed literature.	clinvar
PP2	N/A	PP2 is designated Not Applicable by the InSiGHT MSH6 VCEP v2.0.0.	cspec
PP3	Not met	Multiple in silico predictors indicate a benign effect. The MSH6-specific HCI prior probability for pathogenicity is 0.0008, well below the VCEP PP3_Supporting threshold of >0.68. REVEL score is 0.139 and BayesDel score is -0.503783, both inconsistent with a damaging prediction. SpliceAI delta score is 0.09, indicating no splicing impact.	hci_prior revel bayesdel spliceai
PP4	Not met	No MSI-H tumor data with MMR protein expression loss consistent with an MSH6 defect are reported for this variant. The VCEP PP4 threshold of ≥1 CRC/endometrial MSI-H tumor is not met.	clinvar
PP5	N/A	PP5 is designated Not Applicable by the InSiGHT MSH6 VCEP v2.0.0.	cspec
BA1	Not met	The gnomAD v4.1 allele frequency of 1.24e-06 (0.000124%) is far below the VCEP BA1 Stand-Alone threshold of ≥0.0022 (0.22%).	gnomad_v4
BS1	Not met	The gnomAD v4.1 allele frequency of 1.24e-06 (0.000124%) is below the VCEP BS1 Strong threshold of ≥0.00022 (0.022%).	gnomad_v4
BS2	Not met	No observation of this variant in trans with a known pathogenic MSH6 variant in a patient with CRC after age 45 without CMMRD features has been reported.	clinvar
BS3	Not met	No variant-specific functional assay data demonstrating benign or normal function for NM_000179.3:c.643G>C are available. The variant is absent from the VCEP functional assay documentation spreadsheet.	vcep_functional_assay_svi_documentation_mmr hci_prior
BS4	Not met	No co-segregation data are available to assess lack of segregation with disease for NM_000179.3:c.643G>C.	clinvar
BP1	N/A	BP1 is designated Not Applicable by the InSiGHT MSH6 VCEP v2.0.0.	cspec
BP2	N/A	BP2 is designated Not Applicable by the InSiGHT MSH6 VCEP v2.0.0.	cspec
BP4	Met	Multiple computational predictors support a benign effect. The MSH6-specific HCI prior probability for pathogenicity is 0.0008, which falls below the VCEP BP4_Supporting threshold of <0.11. SpliceAI predicts no splicing impact (max delta score = 0.09, ≤0.1). REVEL score is 0.139 and BayesDel score is -0.503783, both consistent with a benign prediction.	hci_prior spliceai revel bayesdel
BP5	Not met	No tumor data demonstrating MSS status or inconsistent MMR protein expression are available for this variant. The VCEP BP5 thresholds for MSS tumors are not met.	clinvar
BP6	N/A	BP6 is designated Not Applicable by the InSiGHT MSH6 VCEP v2.0.0 as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BP7	N/A	BP7 applies only to synonymous (silent) or intronic variants at or beyond -21/+7. NM_000179.3:c.643G>C is a missense variant (p.Val215Leu) and does not meet the VCEP BP7 criteria.	cspec

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