Variant classification summary

NM_000179.2:c.188C>T

MSH6 · NP_000170.1:p.(Ser63Phe) · NM_000179.2

GRCh37: chr2:48010560 C>T · GRCh38: chr2:47783421 C>T

Gene: MSH6 Transcript: NM_000179.2

Final call

PM2 supporting BP4 supporting benign

Variant details

Gene

MSH6

Transcript

NM_000179.2

Protein

NP_000170.1:p.(Ser63Phe)

gnomAD AF

6.625061281816857e-07 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000179.2:c.188C>T (p.Ser63Phe) is a missense variant in MSH6 exon 1. The variant is extremely rare, observed in 1 of 1,509,420 alleles (AF = 6.625e-07) in gnomAD v4.1 and absent from gnomAD v2.1, meeting PM2_Supporting under the InSiGHT MSH6 VCEP v2.0.0 framework.

2

Multiple in silico predictors are consistent with a benign effect. The HCI prior probability for p.Ser63Phe is 0.003, meeting BP4_Supporting (threshold < 0.11). REVEL score is 0.195, BayesDel score is -0.269, and SpliceAI predicts no splicing impact (max delta = 0.00).

3

PVS1 is not applicable (missense variant). PS1 is not met (no alternate nucleotide change encoding p.Ser63Phe classified as P/LP by this VCEP). PM5 is not met because PP3 is not supporting (HCI prior 0.003, far below PP3_Supporting threshold of >0.68). Multiple VCEP criteria are explicitly Not Applicable: PS4, PP5, PM1, PM6, PP2, BP1, BP2, BP6.

4

The variant has been reported in ClinVar as Uncertain significance by two clinical laboratories (VariationID: 1053294). It has been observed in somatic cancers (COSMIC COSV52275784, n = 6). No variant-specific functional data, segregation data, de novo occurrences, or tumor phenotype data were identified.

5

At present, the only scored criteria are PM2_Supporting (pathogenic) and BP4_Supporting (benign), which offset. Multiple criteria remain unassessed due to absence of clinical, functional, and segregation data. Comprehensive assessment awaits functional assay results for p.Ser63Phe, tumor MSI/IHC data from variant carriers, and segregation analysis.

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	NM_000179.2:c.188C>T is a missense substitution (p.Ser63Phe), not a null variant (nonsense, frameshift, canonical splice, or initiation codon). PVS1 is not applicable to missense variants under either the MSH6 VCEP framework or generic ACMG/AMP guidelines.	pvs1_variant_assessment cspec
PS1	Not met	No alternative nucleotide change encoding p.Ser63Phe has been classified by the InSiGHT Hereditary Colorectal Cancer/Polyposis EP as Pathogenic or Likely Pathogenic. The only nucleotide substitution producing p.Ser63Phe is c.188C>T itself. The VCEP pilot variants spreadsheet contains no entries at codon 63 of MSH6.	cspec hci_prior
PS2	Not assessed	No de novo occurrence with confirmed parentage has been identified for NM_000179.2:c.188C>T in the available literature, ClinVar submissions, or databases. The exploratory literature search found no de novo reports.
PS3	Not assessed	No calibrated functional assay data for p.Ser63Phe was identified in the VCEP functional assay documentation spreadsheet or in available literature. Kariola et al. 2014 (PMID:24362816) performed a functional complementation assay for 74 MSH6 missense variants but the full text is not available to confirm whether p.Ser63Phe was among those tested or what the result was. OncoKB reports no variant-specific reviewed functional evidence.	oncokb
PS4	N/A	The ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis EP Specifications for MSH6 Version 2.0.0 explicitly marks PS4 as Not Applicable for this VCEP.	cspec
PS5	N/A	The ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis EP Specifications for MSH6 Version 2.0.0 explicitly marks PP5 as Not Applicable for this VCEP.	cspec
PM1	N/A	The ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis EP Specifications for MSH6 Version 2.0.0 explicitly marks PM1 as Not Applicable for this VCEP.	cspec
PM2	Met	NM_000179.2:c.188C>T is extremely rare in gnomAD v4.1 (1/1,509,420 alleles; AF = 6.625e-07), meeting the MSH6 VCEP PM2_Supporting threshold of allele frequency < 0.00002 (fewer than 1 in 50,000 alleles). The variant is absent from gnomAD v2.1 and absent from all populations except a single European (non-Finnish) allele.	gnomad_v4 gnomad_v2 cspec
PM5	Not met	The MSH6 VCEP PM5 rule requires PP3 to be supporting for the missense change as a prerequisite. PP3 is not met for p.Ser63Phe (HCI prior probability = 0.003, far below the 0.68 threshold for PP3_Supporting). Therefore PM5 cannot be applied regardless of whether a same-residue comparator exists.	cspec hci_prior
PM6	N/A	The ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis EP Specifications for MSH6 Version 2.0.0 explicitly marks PM6 as Not Applicable for this VCEP.	cspec
PP1	Not assessed	No co-segregation data with disease in pedigrees has been identified for NM_000179.2:c.188C>T. The variant is extremely rare, and no published multiplex families demonstrating variant-disease tracking were found.
PP2	N/A	The ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis EP Specifications for MSH6 Version 2.0.0 explicitly marks PP2 as Not Applicable for this VCEP.	cspec
PP3	Not met	The HCI prior probability for p.Ser63Phe is 0.003, which falls far below the MSH6 VCEP PP3_Supporting threshold of >0.68. REVEL score is 0.195 and BayesDel score is -0.269, both consistent with a benign in silico prediction. SpliceAI predicts no splicing impact (max delta = 0.00). Multiple in silico tools collectively do not support a pathogenic classification.	hci_prior revel bayesdel spliceai cspec
PP4	Not assessed	No tumor MSI/IHC data for patients harboring NM_000179.2:c.188C>T was identified in the available evidence. The criterion requires CRC/Endometrial MSI-H tumors and/or loss of MMR protein expression consistent with the variant location.
PP5	N/A	The ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis EP Specifications for MSH6 Version 2.0.0 explicitly marks PP5 as Not Applicable for this VCEP.	cspec
BA1	Not met	The MSH6 VCEP BA1 threshold requires gnomAD v4 Grpmax filtering allele frequency ≥ 0.0022 (0.22%). The variant has an allele frequency of 6.625e-07 (0.000066%) in gnomAD v4.1, far below this threshold.	gnomad_v4 cspec
BS1	Not met	The MSH6 VCEP BS1 threshold requires gnomAD v4 Grpmax filtering allele frequency ≥ 0.00022 (0.022%). The variant has an allele frequency of 6.625e-07 (0.000066%) in gnomAD v4.1, well below this threshold.	gnomad_v4 cspec
BS2	Not assessed	No evidence of co-occurrence in trans with a known pathogenic MSH6 variant in a patient with colorectal cancer after age 45 without CMMRD features has been identified.
BS3	Not assessed	No calibrated functional assay data demonstrating proficient MMR function for p.Ser63Phe is available. The VCEP functional assay documentation spreadsheet does not list this variant. Kariola et al. 2014 (PMID:24362816) may contain relevant data but full text is unavailable for verification.
BS4	Not assessed	No lack-of-segregation data (variant present in unaffected family members) has been identified for NM_000179.2:c.188C>T.
BP1	N/A	The ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis EP Specifications for MSH6 Version 2.0.0 explicitly marks BP1 as Not Applicable for this VCEP.	cspec
BP2	N/A	The ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis EP Specifications for MSH6 Version 2.0.0 explicitly marks BP2 as Not Applicable for this VCEP.	cspec
BP4	Met	The HCI prior probability for p.Ser63Phe is 0.003, meeting the MSH6 VCEP BP4_Supporting threshold of < 0.11. Multiple in silico predictors are consistent with a benign effect: REVEL score is 0.195 (below typical pathogenic threshold), BayesDel score is -0.269 (negative, favoring benign), and SpliceAI predicts no splicing impact (max delta = 0.00).	hci_prior revel bayesdel spliceai cspec
BP5	Not assessed	No tumor data (CRC/Endometrial MSS status, MMR protein expression, BRAF V600E, or MLH1 methylation) is available for patients harboring NM_000179.2:c.188C>T.
BP6	N/A	The ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis EP Specifications for MSH6 Version 2.0.0 explicitly marks BP6 as Not Applicable, as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BP7	Not met	NM_000179.2:c.188C>T is a missense variant (p.Ser63Phe), not a synonymous (silent) or intronic variant at or beyond -21/+7. BP7 applies only to synonymous and intronic variants.	cspec

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