Variant classification summary

NM_000251.3:c.630G>A

MSH2 · NP_000242.1:p.(Met210Ile) · NM_000251.3

GRCh37: chr2:47637496 G>A · GRCh38: chr2:47410357 G>A

Gene: MSH2 Transcript: NM_000251.3

Final call

VUS

BP4 supporting

Variant details

Gene

MSH2

Transcript

NM_000251.3

Protein

NP_000242.1:p.(Met210Ile)

gnomAD AF

6.196170766466324e-06 (v4.1)

ClinVar

Likely benign

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000251.3:c.630G>A (p.Met210Ile) is a rare missense variant in MSH2 exon 3 observed at extremely low frequency in gnomAD v4.1 (AF = 6.20e-06; 10/1,613,900 alleles; grpmax FAF = 4.37e-05). The grpmax filtering AF exceeds the VCEP PM2_supporting threshold of <2e-05, so PM2 is not met.

2

Computational evidence supports a benign interpretation: the HCI prior probability of pathogenicity is 0.0035, meeting the VCEP BP4_supporting threshold of <0.11. SpliceAI predicts no splicing impact (max delta = 0.04). REVEL score is 0.4 and BayesDel score is -0.059, both consistent with a neutral prediction.

3

No functional data specific to p.M210I were retrievable from the calibrated deep mutational scan by Jia et al. (2021, PMID 33357406), though this assay is recognized by the VCEP SVI documentation. PS3 and BS3 remain not assessed pending retrieval of the variant-specific LOF score from the study's supplementary data.

4

This variant has been reported in ClinVar as Likely benign by Ambry Genetics and Benign by Invitae (ClinVar ID 577710, review status: criteria provided, single submitter, 1-star). However, PP5 and BP6 are explicitly not applicable under the InSiGHT MMR VCEP v2.0, and the review status does not meet 3-star expert panel criteria.

5

No tumor pathology, segregation, de novo, or case-control data were available for this variant. Criteria dependent on clinical or family-level evidence (PS2, PP1, PP4, BS2, BS4, BP5) could not be assessed.

6

Under the InSiGHT MMR VCEP v2.0 combining rules, the single BP4_supporting criterion does not meet the threshold for Likely Benign (≥2 supporting benign criteria required per Rule 19) or Benign classification. The variant is classified as a Variant of Uncertain Significance.

Final determination: No criteria-combination rule matched the adjudicated criteria in the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH2 Version 2.0 v2.0 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.630G>A is a missense variant (p.Met210Ile). PVS1 applies only to null variants (nonsense, frameshift, canonical ±1,2 splice sites) per the InSiGHT MMR VCEP v2.0 decision tree. This substitution does not fall into any PVS1-eligible variant bucket.	pvs1_generic_framework
PS1	Not met	c.630G>A encodes p.Met210Ile. No alternate nucleotide change at codon 630 producing the same amino acid change (Met210Ile) has been classified as Pathogenic or Likely Pathogenic by the InSiGHT MMR VCEP. No evidence of any other nucleotide substitution resulting in M210I with a prior P/LP classification was identified in ClinVar or VCEP pilot variant records.	clinvar vcep_vcep_pilot_variants_mmr
PS2	Not assessed	No de novo data are available for this variant. No reports of confirmed de novo occurrence of NM_000251.3:c.630G>A with maternity and paternity confirmed were found in ClinVar, the literature packet, or the evidence brief.	clinvar
PS3	Not assessed	PMID 33357406 (Jia et al. 2021) provides a calibrated functional assay via deep mutational scanning of MSH2 recognized by the InSiGHT MMR VCEP SVI documentation (22 P/LP validation controls, LOF score threshold >0.4 for abnormal readout). However, the variant NM_000251.3:c.630G>A (p.M210I) is not individually reported in the full-text narrative, and its specific LOF score or calibrated functional odds could not be retrieved from the available data. Without the variant-specific functional score, PS3 cannot be applied.	PMID:33357406 vcep_functional_assay_svi_documentation_mmr
PS4	N/A	The InSiGHT MMR VCEP v2.0 explicitly marks PS4 as Not Applicable for MMR variant classification, citing the availability of tumor IHC data through PP4 as the preferred approach.	cspec
PS5	N/A	PS5 is not part of the InSiGHT MMR VCEP specification v2.0. The criterion is not used by this expert panel framework.	cspec
PM1	N/A	The InSiGHT MMR VCEP v2.0 explicitly states PM1 is Not Applicable: '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	Not met	The VCEP PM2_supporting threshold requires gnomAD v4 grpmax filtering allele frequency < 0.00002 (<1 in 50,000 alleles). The observed gnomAD v4.1 grpmax FAF for this variant is 4.369e-05 (4.37 × 10⁻⁵), which exceeds the threshold. Although the variant is very rare (total AF = 6.20e-06; 10/1,613,900 alleles), the grpmax filtering AF does not meet the VCEP-defined cutoff.	gnomad_v4 cspec
PM5	Not met	VCEP PM5 requires a different missense change at the same amino acid residue (Met210) classified as Pathogenic or Likely Pathogenic by the InSiGHT VCEP at the protein level. No such comparator was identified. The pm5_candidates search returned no same-residue candidates. Furthermore, VCEP PM5 requires PP3 to be supporting, which is also not met (HCI prior = 0.0035, far below the >0.68 threshold).	cspec clinvar pm5_candidates
PM6	N/A	The InSiGHT MMR VCEP v2.0 marks PM6 as Not Applicable. De novo evidence is assessed through PS2 in this framework.	cspec
PP1	Not assessed	No co-segregation data are available for this variant. No pedigree information or Bayes likelihood ratios for co-segregation were found in the case evidence, ClinVar submissions, or literature.	clinvar
PP2	N/A	The InSiGHT MMR VCEP v2.0 explicitly marks PP2 as Not Applicable: 'Missense variant in a gene with low rate of benign missense changes does not apply.'	cspec
PP3	Not met	The HCI prior probability of pathogenicity for c.630G>A (p.M210I) is 0.0035, as reported in the local HCI-PRIORS-MSH2 lookup table. This value is well below the VCEP PP3_supporting threshold of >0.68. SpliceAI delta score is 0.04, below the 0.2 threshold for non-canonical splice prediction.	hci_prior spliceai cspec
PP4	Not assessed	No tumor MSI/IHC data are available for this variant. The VCEP PP4 criterion requires evidence of MSI-H colorectal/endometrial tumors and/or loss of MMR protein expression consistent with MSH2 variant location. No such clinical data were provided in the case evidence, ClinVar submissions, or literature.	clinvar
PP5	N/A	The InSiGHT MMR VCEP v2.0 explicitly marks PP5 as 'Not Applicable for this VCEP' per the ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation. ClinVar review status is 'criteria provided, single submitter' (1-star), not 3-star expert panel, so PP5 would not be met even under a generic fallback.	cspec clinvar
BA1	Not met	The VCEP BA1 threshold requires gnomAD v4 grpmax filtering allele frequency ≥ 0.001 (0.1%). The observed grpmax FAF is 4.369e-05, far below this threshold. This variant is too rare in population databases to qualify as a common benign polymorphism.	gnomad_v4 cspec
BS1	Not met	The VCEP BS1 threshold requires gnomAD v4 grpmax filtering allele frequency ≥ 0.0001 (0.01%). The observed grpmax FAF is 4.369e-05, which is below this threshold. The variant does not meet the population frequency cutoff for BS1.	gnomad_v4 cspec
BS2	Not assessed	No evidence of co-occurrence in trans with a known pathogenic MSH2 variant was found. The VCEP BS2 rule requires confirmed phase with a pathogenic variant in trans in a patient with colorectal cancer after age 45 (or other LS cancer above median age of onset) without CMMRD features.	clinvar
BS3	Not assessed	PMID 33357406 (Jia et al. 2021) provides a calibrated functional assay for MSH2 recognized by the VCEP SVI documentation. However, the specific functional odds or LOF score for p.M210I were not retrievable from the full text. Without the variant-specific calibrated functional readout, BS3 cannot be applied.	PMID:33357406 vcep_functional_assay_svi_documentation_mmr
BS4	Not assessed	No segregation data demonstrating lack of co-segregation with disease are available. VCEP BS4 requires pedigree-based Bayes likelihood ratios showing lack of co-segregation.
BP1	N/A	The InSiGHT MMR VCEP v2.0 explicitly marks BP1 as Not Applicable: 'Missense variant in a gene where only loss of function causes disease is not applicable.'	cspec
BP2	N/A	The InSiGHT MMR VCEP v2.0 explicitly marks BP2 as Not Applicable. BS2 is used instead for co-occurrence evidence.	cspec
BP4	Met	The HCI prior probability of pathogenicity for c.630G>A (p.M210I) is 0.0035, which is below the VCEP BP4_supporting threshold of <0.11. This indicates that computational evidence predicts no damaging effect on the gene product, supporting a benign interpretation.	hci_prior cspec
BP5	Not assessed	No tumor data are available demonstrating MSS status or no loss of MMR protein expression. The VCEP BP5 criterion requires tumor evidence inconsistent with the variant causing disease (MSS tumors, no loss of MMR expression, BRAF V600E/MLH1 methylation in context).
BP6	N/A	The InSiGHT MMR VCEP v2.0 explicitly marks BP6 as 'Not Applicable for this VCEP' per the ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation. ClinVar review status is 'criteria provided, single submitter' (1-star), not 3-star expert panel, so BP6 would not be met even under generic fallback.	cspec clinvar
BP7	N/A	BP7 applies only to synonymous (silent) or intronic variants at or beyond -21/+7 per the VCEP specification. NM_000251.3:c.630G>A is a missense variant (p.Met210Ile) and is therefore not eligible for BP7.	cspec

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