Variant classification summary

NM_000251.3:c.2197G>A

MSH2 · NP_000242.1:p.(Ala733Thr) · NM_000251.3

GRCh37: chr2:47703697 G>A · GRCh38: chr2:47476558 G>A

Gene: MSH2 Transcript: NM_000251.3

Final call

VUS

BS1 strong

Variant details

Gene

MSH2

Transcript

NM_000251.3

Protein

NP_000242.1:p.(Ala733Thr)

gnomAD AF

3.593315936727902e-05 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

The InSiGHT MMR VCEP BS1_Strong criterion is met: gnomAD v4.1 grpmax filtering allele frequency of 0.033% (0.00033148) falls within the 0.01-0.1% range defined for BS1_Strong, and the variant is not consistent with a founder effect.

2

PM2_Supporting is not met: the gnomAD v4.1 allele frequency of 0.0036% exceeds the VCEP threshold of < 0.002% (< 1 in 50,000 alleles).

3

PP3 is not met: the HCI prior probability of 0.3778 is below the PP3_Supporting threshold of > 0.68, and SpliceAI predicts no splicing impact (delta = 0.00).

4

PVS1 is not applicable: this is a missense variant (p.Ala733Thr), not a null variant, and does not meet any PVS1 rule under the MMR VCEP decision tree.

5

PS3 remains not assessed: the VCEP-calibrated functional assay (PMID:33357406) likely includes this variant but variant-specific confirmation was not available in this review.

6

Under the InSiGHT MMR VCEP v2.0.0 combining rules, a single BS1_Strong criterion without any opposing pathogenic criteria results in a classification of Likely Benign (Rule 18: 1 Strong Benign + 1 Supporting Benign; or Rule 19: >= 2 Supporting Benign). However, with no supporting benign criteria met beyond BS1_Strong and PS3/PP1/PP4 unresolved, the provisional classification is Likely Benign pending functional data resolution.

Final determination: No criteria-combination rule matched the adjudicated criteria in the Richards et.al., 2015 - Combining rules v2.0.0 framework, so the variant remains a Variant of Uncertain Significance pending human review.

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_000251.3:c.2197G>A is a missense variant (p.Ala733Thr), not a null variant (nonsense, frameshift, or canonical splice site). Per InSiGHT MMR VCEP v2.0.0, PVS1 applies only to null variants and specific splice aberrations. Missense substitutions are not eligible for PVS1 under this framework.	pvs1_generic_framework cspec
PS1	Not met	No alternative nucleotide change at codon 733 resulting in the same amino acid substitution (p.Ala733Thr) has been classified as Pathogenic or Likely Pathogenic by the InSiGHT MMR VCEP. Without such a comparator variant meeting the VCEP criteria, PS1 cannot be applied.	cspec
PS2	Not met	No de novo occurrences of NM_000251.3:c.2197G>A have been identified in any reviewed publication or database entry with confirmed parentage. The InSiGHT MMR VCEP PS2 point system cannot be applied without documented de novo observations.	cspec
PS3	Not assessed	The InSiGHT MMR VCEP functional assay documentation lists calibrated assays relevant to MSH2 missense variants (PMID:33357406, Jia/Scott 2021, LOF score > 0.4 threshold for PS3). The exploratory evidence scan suggests this variant was likely included in the massively parallel functional testing. However, full-text confirmation that the exact variant c.2197G>A (p.Ala733Thr) was tested and the specific measured readout (LOF score or MMR activity percentage) could not be verified — no full-text publications were available for any cited PMID. PS3 remains not_assessed pending retrieval and review of PMID:33357406 supplementary data.	cspec vcep_functional_assay_svi_documentation_mmr
PS4	N/A	PS4 is designated Not Applicable by the InSiGHT MMR VCEP v2.0.0 specification for MSH2.	cspec
PS5	N/A	PS5 is not defined in the InSiGHT MMR VCEP v2.0.0 specification for MSH2 and is superseded by VCEP-specific criteria.	cspec
PM1	N/A	PM1 is designated Not Applicable by the InSiGHT MMR VCEP v2.0.0 specification for MSH2.	cspec
PM2	Not met	The InSiGHT MMR VCEP PM2_Supporting threshold requires allele frequency < 0.00002 (< 1 in 50,000 alleles) in gnomAD v4. The observed gnomAD v4.1 allele frequency is 3.59e-05 (58/1,614,108 alleles), which exceeds this threshold. PM2 is not met.	gnomad_v4 cspec
PM3	N/A	PM3 is trivially not applicable for this assessment per user directive. PM3 applies to recessive disorders with biallelic observations; MSH2-associated Lynch syndrome is autosomal dominant, and no CMMRD biallelic data was identified for this variant.
PM4	N/A	PM4 is trivially not applicable: this is a substitution variant, not a non-frameshift deletion/insertion or stop-loss variant.
PM5	Not met	The InSiGHT MMR VCEP PM5 rule requires that PP3 be supporting for the missense change before PM5 can be applied. PP3 is not met for this variant (HCI prior probability 0.3778, below the 0.68 PP3_Supporting threshold). Therefore PM5 cannot be applied regardless of whether a comparator variant exists.	cspec hci_prior
PM6	N/A	PM6 is designated Not Applicable by the InSiGHT MMR VCEP v2.0.0 specification for MSH2.	cspec
PP1	Not assessed	The InSiGHT database reportedly classifies this variant as pathogenic (Class 5), which suggests segregation data may have been considered. However, no specific published pedigrees with co-segregation analysis of c.2197G>A were confirmed in available full-text or abstracts. Co-segregation evidence cannot be applied without verified family data and Bayes Likelihood Ratio calculations.	cspec
PP2	N/A	PP2 is designated Not Applicable by the InSiGHT MMR VCEP v2.0.0 specification for MSH2.	cspec
PP3	Not met	The InSiGHT MMR VCEP PP3 rule uses HCI prior probability: > 0.81 for PP3_Moderate, > 0.68 and <= 0.81 for PP3_Supporting. The HCI prior for this variant is 0.3778, which does not meet either threshold. SpliceAI delta score is 0.0, also not meeting the PP3 threshold for non-canonical splice variants. REVEL score is 0.851 (high) but REVEL is not used in the VCEP PP3 framework.	hci_prior spliceai cspec revel
PP4	Not assessed	The InSiGHT MMR VCEP PP4 requires MSI-H tumors and/or loss of MMR protein expression consistent with the variant location in independent CRC/endometrial tumors. No specific patient-level PP4 data (MSI status, IHC results) were identified in the reviewed literature for this variant. The InSiGHT pilot classification for similar variants suggests PP4 may have been applied in expert panel review, but variant-specific clinical data were not verified.	cspec
PP5	N/A	PP5 is designated Not Applicable by the InSiGHT MMR VCEP v2.0.0 specification for MSH2.	cspec
BA1	Not met	The InSiGHT MMR VCEP BA1 threshold requires gnomAD v4 Grpmax filtering allele frequency >= 0.001 (0.1%). The observed gnomAD v4.1 grpmax FAF is 0.00033148 (0.033%), which is below the BA1 threshold.	gnomad_v4 cspec
BS1	Met	The InSiGHT MMR VCEP BS1_Strong threshold is gnomAD v4 Grpmax filtering allele frequency >= 0.0001 and < 0.001 (0.01-0.1%), with exclusion as a founder pathogenic variant. The gnomAD v4.1 grpmax FAF is 0.00033148 (0.033%), which falls within this range. The variant's distribution across multiple East Asian subpopulations and absence from non-Asian populations does not suggest a founder effect.	gnomad_v4 cspec
BS2	Not met	The InSiGHT MMR VCEP BS2 requires co-occurrence in trans with a known pathogenic MSH2 variant in a patient with LS-spectrum cancer after age 45 without CMMRD features. No such co-occurrence data was identified in the reviewed literature or databases for this variant.	cspec
BS3	Not met	The InSiGHT MMR VCEP BS3 requires calibrated functional assays showing functional odds for pathogenicity <= 0.05 (BS3_Strong) or > 0.05 and <= 0.48 (BS3_Supporting), or variant-specific proficient function per the MMR functional assay flowchart. The exploratory evidence scan indicates that available functional data (PMID:33357406, Thompson et al. 2014) supports a damaging effect rather than normal function. No evidence of proficient MMR function for this variant was identified.	cspec vcep_functional_assay_svi_documentation_mmr
BS4	Not met	The InSiGHT MMR VCEP BS4 requires lack of co-segregation with disease in pedigrees with a combined Bayes Likelihood Ratio meeting specified thresholds. No pedigree demonstrating lack of co-segregation was identified in the reviewed literature for this variant.	cspec
BP1	N/A	BP1 is designated Not Applicable by the InSiGHT MMR VCEP v2.0.0 specification for MSH2.	cspec
BP2	N/A	BP2 is designated Not Applicable by the InSiGHT MMR VCEP v2.0.0 specification for MSH2.	cspec
BP3	N/A	BP3 is designated Not Applicable by the InSiGHT MMR VCEP v2.0.0 specification for MSH2. This is an in-frame deletion/insertion criterion not relevant to a missense substitution.	cspec
BP4	Not met	The InSiGHT MMR VCEP BP4_Supporting threshold requires HCI prior probability < 0.11 for missense variants. The HCI prior for this variant is 0.3778, which exceeds this threshold. The SpliceAI delta score of 0.0 is relevant only for intronic and synonymous variants per the VCEP rule. REVEL score of 0.851 and BayesDel score of 0.273 are not used in the VCEP BP4 framework.	hci_prior spliceai cspec revel bayesdel
BP5	Not met	The InSiGHT MMR VCEP BP5 requires MSS tumors and/or absence of MMR protein expression loss in LS spectrum tumors. No such evidence was identified for this variant in the reviewed literature or databases.	cspec
BP6	N/A	BP6 is designated Not Applicable by the InSiGHT MMR VCEP v2.0.0 specification for MSH2.	cspec
BP7	N/A	BP7 applies only to synonymous (silent) or intronic variants at or beyond -21/+7. NM_000251.3:c.2197G>A is a missense substitution (p.Ala733Thr), not a synonymous or intronic variant.	cspec

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