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MSH2
Final classification
VUS
MSH2 c.630G>A · p.Met210Ile
MSH2

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.

Gene
MSH2
Transcript
NM_000251.3
HGVS · transcript:coding
NM_000251.3:c.630G>A
Consequence
N/A
GRCh38
chr2:47410357 G>A
GRCh37
chr2:47637496 G>A
Basis ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH2 Version 2.0 v2.0 criteria-combination framework was evaluated deterministically with applied criteria: BP4 supporting; no rule matched the adjudicated criteria.
ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MSH2 Version 2.0 v2.0 criteria-combination framework was evaluated deterministically with applied criteria: BP4 supporting; no rule matched the adjudicated criteria.
Classification rationale
BP4 VUS
MSH2 c.630G>A

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.1 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.2 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.3 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.4 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.5 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.6

BP4 VUS
2 hci_priorspliceai ↗revelbayesdelcspec ↗
3 PMID:33357406 ↗vcep_functional_assay_svi_documentation_mmr
Gene diagram · NM_000251.3 · variants mapped to exon structure
MSH2 NM_000251.3
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 14 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
BP4 supporting Benign
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 probability = 0.0035well below the VCEP BP4_supporting threshold of <0.11. SpliceAI max delta = 0.04 (<0.1) confirms no predicted splicing impact.
Assessed · not applied
Pathogenic
PS1 c.630G>A encodes p.Met210Ile.
PS2 No de novo data are available for this variant.
PS3 PMID 33357406 (Jia et al.
PM2 The VCEP PM2_supporting threshold requires gnomAD v4 grpmax filtering allele frequency < 0.00002 (<1 in 50,000 alleles).
PM5 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.
PP1 No co-segregation data are available for this variant.
PP3 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.
PP4 No tumor MSI/IHC data are available for this variant.
Benign
BA1 The VCEP BA1 threshold requires gnomAD v4 grpmax filtering allele frequency ≥ 0.001 (0.1%).
BS1 The VCEP BS1 threshold requires gnomAD v4 grpmax filtering allele frequency ≥ 0.0001 (0.01%).
BS2 No evidence of co-occurrence in trans with a known pathogenic MSH2 variant was found.
BS3 PMID 33357406 (Jia et al.
BS4 No segregation data demonstrating lack of co-segregation with disease are available.
BP5 No tumor data are available demonstrating MSS status or no loss of MMR protein expression.
N/A · 10 PVS1 · PS4 · PM1 · PM6 · PP2 · PP5 · BP1 · BP2 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 6.19617e-06; MAF= 0.00062%, 10/1613900 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 8.78484e-05; MAF= 0.00878%, 8/91066 alleles, homozygotes = 0); grpmax FAF= 4.369e-05.
v2.1
This variant is present in gnomAD v2.1 (AF= 7.97951e-06; MAF= 0.00080%, 2/250642 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 6.53253e-05; MAF= 0.00653%, 2/30616 alleles, homozygotes = 0); grpmax FAF= 1.082e-05.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00062% · 10 / 1,613,900
0 hom · FAF 0.0044%
South Asian
8 / 91,066
0.0088%
Remaining individuals
1 / 62,486
0.0016%
European (non-Finnish)
1 / 1,180,024
8.5e-05%
+ 7 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0008% · 2 / 250,642
0 hom · FAF 0.0011%
South Asian
2 / 30,616
0.0065%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals)
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Likely benign (1 clinical laboratory) and as Benign (1 clinical laboratory). (ClinVarID = 577710)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04). REVEL score = 0.4. BayesDel score = -0.0594243. HCI prior probability for pathogenicity = 0.0035. MAPP score = 4.66. Custom PP2 score = 0.016.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. MSH2, a DNA mismatch repair protein, is frequently mutated in colorectal, small bowel, and endometrial cancers.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV113236220, n = 1 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 3 PMIDs not cited in assessment
33357406 ↗ Massively parallel functional testing of MSH2 missense variants conferring Lynch syndrome risk. CLINVAR
25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR