Variant classification summary

NM_000251.3:c.1619G>C

MSH2 · NP_000242.1:p.(Ser540Thr) · NM_000251.3

GRCh37: chr2:47693905 G>C · GRCh38: chr2:47466766 G>C

Gene: MSH2 Transcript: NM_000251.3

Final call

PM2 supporting BP4 supporting benign

Variant details

Gene

MSH2

Transcript

NM_000251.3

Protein

NP_000242.1:p.(Ser540Thr)

gnomAD AF

8.674456328449615e-06 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000251.3:c.1619G>C (p.Ser540Thr) is a missense variant in MSH2 exon 10. It is extremely rare in population databases (gnomAD v4.1 AF = 8.67e-06, 14/1,613,934 alleles), meeting PM2_Supporting under the InSiGHT MSH2 VCEP v2.0.0 threshold of <0.00002.

2

Multiple lines of computational evidence (HCI prior = 0.0006, SpliceAI max delta = 0.03, REVEL = 0.276, BayesDel = -0.242779) predict a neutral effect, meeting BP4_Supporting under the InSiGHT MSH2 VCEP v2.0.0 threshold of HCI prior < 0.11.

3

Functional data from a calibrated massively parallel assay (PMID:33357406) exists for MSH2 missense variants but the variant-specific LoF score for p.Ser540T could not be verified from the available full text; PS3/BS3 remain not assessed pending supplementary data review.

4

ClinVar reports this variant as Uncertain Significance (3 clinical laboratories) and Benign (1 clinical laboratory), with no expert panel review. PP5 is not applicable under this VCEP.

5

This variant has been observed in COSMIC (n=1 somatic occurrence) but does not lie in a statistically significant mutational hotspot.

Final determination: Rule31 in the Richards et.al., 2015 - Combining rules 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	Missense substitution; not a null variant (nonsense, frameshift, or canonical splice site). PVS1 is restricted to null variants under the InSiGHT MSH2 VCEP v2.0.0 decision tree.	pvs1_variant_assessment pvs1_gene_context
PS1	Not assessed	No evidence found of a different nucleotide change encoding the same amino acid substitution (p.Ser540Thr) previously classified as Pathogenic or Likely Pathogenic by the InSiGHT MSH2 VCEP.
PS2	Not assessed	No de novo data available for this variant. No publications or clinical records report a de novo occurrence of NM_000251.3:c.1619G>C with confirmed maternity and paternity.
PS3	Not assessed	PMID 33357406 (Jia et al. 2021) is a calibrated functional assay for MSH2 missense variants listed in the VCEP Functional-assay-SVI-documentation-MMR.xlsx. The paper reports a massively parallel screen covering 94.4% of possible MSH2 missense variants, but the full text does not name p.Ser540T specifically and the variant-specific LoF score could not be verified from the available text. The supplementary data tables are required to extract the S540T LoF score and determine whether it meets the calibrated functional odds threshold for PS3 (OddsPath > 2.08 for supporting, > 4.3 for moderate, > 18.7 for strong).	PMID:33357406
PS4	N/A	Not applicable under InSiGHT MSH2 VCEP v2.0.0. The VCEP states: 'Due to the availability of tumor IHC data for variant classification (see PP4), PS4 has not been utilized for MMR variant classification using proband counting.'	cspec
PS5	N/A	PS5 is not included as a criterion in the InSiGHT MSH2 VCEP v2.0.0 criteria set and is not available for use in this framework.	cspec
PM1	N/A	Not applicable under InSiGHT MSH2 VCEP v2.0.0. The VCEP states: 'There are no recognized mutational hot spots that could be used for classification purposes. While there are functional domains in the MMR genes, the distribution of pathogenic variants is generalized over all the domains.'	cspec
PM2	Met	This variant is extremely rare in population databases. In gnomAD v4.1, the allele frequency is 8.67e-06 (14/1,613,934 alleles, no homozygotes) with a grpmax filtering allele frequency of 5.42e-06, which is below the InSiGHT MSH2 VCEP PM2_Supporting threshold of <0.00002 (<1 in 50,000 alleles). Absent from gnomAD v2.1 and gnomAD-Canada.	gnomad_v2 gnomad_v4 gnomad_canada cspec
PM5	N/A	No different missense change at codon 540 previously classified as Pathogenic or Likely Pathogenic by the InSiGHT MSH2 VCEP. pm5_candidates.json found no comparator variants at this residue.	pm5_candidates
PM6	N/A	Not applicable under InSiGHT MSH2 VCEP v2.0.0. PM6 is set to 'Not applicable' for all strength levels in the VCEP criteria; PS2 point system is used instead for de novo assessment.	cspec
PP1	Not assessed	No co-segregation data available for this variant. No pedigrees with combined Bayes Likelihood Ratio calculations were identified.
PP2	N/A	Not applicable under InSiGHT MSH2 VCEP v2.0.0. The VCEP states: 'Missense variant in a gene with low rate of benign missense changes does not apply.'	cspec
PP3	Not met	Multiple lines of computational evidence do not support a deleterious effect. The HCI prior probability for pathogenicity is 0.0006, well below the PP3_Supporting threshold of >0.68. SpliceAI delta score is 0.03, well below the 0.2 threshold for predicted splice defects. REVEL score is 0.276, and BayesDel score is -0.242779, both in the neutral/benign range.	hci_prior spliceai revel bayesdel cspec
PP4	Not assessed	No tumor MSI or IHC data available for this variant. The InSiGHT MSH2 VCEP PP4 criterion requires specific numbers of CRC/Endometrial MSI-H tumors with MMR protein expression status consistent with the variant location. No such data were identified in the evidence brief or literature.
PP5	N/A	Not applicable under InSiGHT MSH2 VCEP v2.0.0. The VCEP states: 'This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.'	cspec
BA1	Not met	The gnomAD v4.1 grpmax filtering allele frequency is 5.42e-06, far below the InSiGHT MSH2 VCEP BA1 threshold of >=0.001 (0.1%). The variant is rare in population databases and does not meet the stand-alone benign allele frequency threshold.	gnomad_v4 cspec
BS1	Not met	The gnomAD v4.1 grpmax filtering allele frequency is 5.42e-06, below the InSiGHT MSH2 VCEP BS1 threshold of >=0.0001 (0.01%). The variant is too rare in population databases to meet BS1.	gnomad_v4 cspec
BS2	Not assessed	No evidence of co-occurrence in trans with a known pathogenic MSH2 variant in a patient with colorectal cancer after age 45 without CMMRD features. Confirmation of phase would require parental testing.
BS3	Not assessed	PMID 33357406 (Jia et al. 2021) is a calibrated functional assay for MSH2 missense variants recognized by the VCEP. The paper reports that 89.4% of MSH2 missense variants are functionally neutral. However, the variant-specific LoF score for p.Ser540T could not be verified from the available full text. The supplementary data tables are required to confirm whether the S540T LoF score meets the VCEP BS3_Strong (functional odds <=0.05) or BS3_Supporting (>0.05 & <=0.48) thresholds.	PMID:33357406
BS4	Not assessed	No lack-of-segregation data available for this variant. No pedigrees with combined Bayes Likelihood Ratio calculations were identified to support BS4.
BP1	N/A	Not applicable under InSiGHT MSH2 VCEP v2.0.0. The VCEP states: 'Missense variant in a gene where only loss of function causes disease is not applicable.'	cspec
BP2	N/A	Not applicable under InSiGHT MSH2 VCEP v2.0.0. The VCEP states: 'BS2 is used instead.'	cspec
BP4	Met	Multiple lines of computational evidence suggest no impact on the gene product. The HCI prior probability for pathogenicity is 0.0006, well below the InSiGHT MSH2 VCEP BP4_Supporting threshold of <0.11. SpliceAI predicts no splicing impact (max delta = 0.03, <=0.1). REVEL score is 0.276 (neutral range), and BayesDel score is -0.242779 (benign prediction).	hci_prior spliceai revel bayesdel cspec
BP5	Not assessed	No tumor data available demonstrating MSS status or loss of MMR protein expression inconsistent with MSH2 involvement. The VCEP BP5 criterion requires documented tumors with MSS and/or inconsistent IHC findings.
BP6	N/A	Not applicable under InSiGHT MSH2 VCEP v2.0.0. The VCEP states: 'This criterion is not for use 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_000251.3:c.1619G>C is a missense substitution (p.Ser540Thr), not a synonymous or intronic variant.	cspec
BP3	N/A	Missense substitution; BP3 applies only to in-frame deletions/insertions in a repetitive region without known function.	cspec
PM4	N/A	Missense substitution; PM4 applies to protein length changes from in-frame deletions/insertions or stop-loss variants. The VCEP further specifies that protein length change from in-frame variants is not used due to lack of evidence.	cspec
PM3	N/A	MSH2/Lynch syndrome is autosomal dominant; PM3 (detected in trans with pathogenic variant for recessive disorders) is not applicable in the germline heterozygous context. While the InSiGHT VCEP does define PM3 for CMMRD biallelic assessment, no CMMRD context is indicated for this case.

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