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MSH2
Final classification
Likely Benign
MSH2 c.211+9C>A · p.?
MSH2

This variant is an intronic substitution at c.211+9 in MSH2, located beyond the +7 splice boundary, meeting BP7 (supporting benign).

Gene
MSH2
Transcript
NM_000251.3
HGVS · transcript:coding
NM_000251.3:c.211+9C>A
Consequence
N/A
GRCh38
chr2:47403411 C>A
GRCh37
chr2:47630550 C>A
Basis Richards et.al., 2015 - Combining rules v2.0.0 criteria-combination framework: matched Rule19 (Benign.Supporting >=2) with applied criteria: PM2 supporting, BP4 supporting benign, BP7 supporting benign; maps to Likely Benign.
Richards et.al., 2015 - Combining rules v2.0.0 criteria-combination framework: matched Rule19 (Benign.Supporting >=2) with applied criteria: PM2 supporting, BP4 supporting benign, BP7 supporting benign; maps to Likely Benign.
Classification rationale
PM2 BP4BP7 Likely Benign
MSH2 c.211+9C>A

This variant is an intronic substitution at c.211+9 in MSH2, located beyond the +7 splice boundary, meeting BP7 (supporting benign).1 SpliceAI predicts no splicing impact (max delta = 0.00), meeting BP4 (supporting benign) for intronic variants under the InSiGHT MSH2 VCEP (Walker et al. 2023).2 This variant is present at extremely low frequency in gnomAD v4.1 (overall AF = 5.04 × 10⁻⁶, 8/1,588,690 alleles, 0 homozygotes), meeting PM2 at supporting strength under the InSiGHT MSH2 VCEP threshold of <0.00002.3 The grpmax filtering allele frequency in gnomAD v4.1 is 8.99 × 10⁻⁵ (0.009%), which is below the BS1 threshold (≥ 0.0001) and the BA1 threshold (≥ 0.001); therefore BS1 and BA1 are not met.4 PVS1 is not applicable — this is an intronic variant at +9, not a null variant or canonical splice site variant under the InSiGHT MSH2 VCEP PVS1 decision tree.5 No tumor MSI/IHC, co-segregation, de novo, functional assay, or case-control data are available for this variant. No publications specifically report NM_000251.3:c.211+9C>A. Under the InSiGHT MSH2 VCEP v2.0.0 combining rules, two supporting benign criteria (BP4, BP7) meet Rule 19 (≥ 2 Benign Supporting → Likely Benign). One pathogenic supporting criterion (PM2) is also present but does not trigger a VCEP-defined conflict with benign supporting evidence.6

PM2 + BP4 + BP7 Likely Benign
Gene diagram · NM_000251.3 · variants mapped to exon structure
MSH2 NM_000251.3
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 12 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is present at extremely low frequency in gnomAD v4.1 (overall allele frequency = 5.04 × 10⁻⁶; 8/1,588,690 alleles; 0 homozygotes), which is below the InSiGHT MSH2 VCEP threshold of <0.00002 (<1 in 50,000 alleles). Highest subpopulation frequency is in East Asian (AF = 0.000182; 8/43,960).
gnomAD v4.1 AF = 5.036e-06below VCEP PM2 threshold of <0.00002
BP4 supporting Benign
SpliceAI predicts no splicing impact for this intronic variant (max delta score = 0.00 ≤ 0.1), meeting the InSiGHT MSH2 VCEP BP4 rule for intronic and synonymous variants as per Walker et al. 2023.
SpliceAI max delta = 0.00at or below the VCEP BP4 threshold of ≤ 0.1
BP7 supporting Benign
This variant is intronic at position c.211+9, which is beyond +7 from the 3' end of exon 1, meeting the InSiGHT MSH2 VCEP BP7 rule for intronic variants at or beyond the -21/+7 boundaries. This variant may satisfy both BP7 and BP4.
Intronic variant at c.211+9 positionbeyond the +7 exon boundary
Assessed · not applied
Pathogenic
PS1 No known pathogenic variant at the same non-canonical splice nucleotide (c.211+9) in MSH2.
PS2 No de novo reports available for NM_000251.3:c.211+9C>A.
PS3 No functional assay data available for this intronic variant.
PP1 No co-segregation data available for this variant.
PP3 For intronic variants, the InSiGHT MSH2 VCEP PP3 requires a SpliceAI delta score ≥ 0.2 for non-canonical splice nucleotides (Supporting strength).
PP4 No tumor MSI or immunohistochemistry data available for this variant.
Benign
BA1 gnomAD v4.1 grpmax filtering allele frequency is 8.99 × 10⁻⁵ (0.009%), which is below the InSiGHT MSH2 VCEP BA1 threshold of ≥ 0.001 (≥ 0.1%).
BS1 gnomAD v4.1 grpmax filtering allele frequency is 8.99 × 10⁻⁵ (0.009%), which is below the InSiGHT MSH2 VCEP BS1 threshold of ≥ 0.0001 (0.01%).
BS2 No evidence of this variant occurring in trans with a known pathogenic MSH2 variant in a patient with colorectal cancer after age 45 and no CMMRD features.
BS3 No laboratory functional assay data available confirming absence of mRNA aberration or proficient MMR function for this specific intronic variant.
BS4 No lack-of-segregation data available.
BP5 No tumor data available to assess MSS status, MMR protein expression, BRAF V600E, or MLH1 methylation.
N/A · 11 PVS1 · PS4 · PM1 · PM5 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP6
Research & evidence
Population frequency · supports benign
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= 5.0356e-06; MAF= 0.00050%, 8/1588690 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 0.000181984; MAF= 0.01820%, 8/43960 alleles, homozygotes = 0); grpmax FAF= 8.994e-05.
v2.1
This variant is present in gnomAD v2.1 (AF= 1.87447e-05; MAF= 0.00187%, 4/213394 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 0.000249626; MAF= 0.02496%, 4/16024 alleles, homozygotes = 0); grpmax FAF= 8.497e-05.
🇨🇦 CA
Not available in gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0005% · 8 / 1,588,690
0 hom · FAF 0.009%
East Asian
8 / 43,960
0.018%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
gnomAD v2.1
0.0019% · 4 / 213,394
0 hom · FAF 0.0085%
East Asian
4 / 16,024
0.025%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
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 (4 clinical laboratories) and as Uncertain significance (1 clinical laboratory). (ClinVarID = 237381)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional No data
No calibrated functional assay or RNA evidence was identified for this variant.
OncoKB ↗
COSMIC screenshot
COSMIC
Somatic evidence
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant cancer hotspot.
COSMIC ↗
Sources & reference links
8Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Triaged references · 7 PMIDs not cited in assessment
15662714 ↗ Identification of Muir-Torre syndrome among patients with sebaceous tumors and keratoacanthomas: role of clinical features, microsatellite instability, and immunohistochemistry. CLINVAR
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR
23535968 ↗ Informing family members of individuals with Lynch syndrome: a guideline for clinical geneticists. CLINVAR
25356965 ↗ ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing. CLINVAR
25452455 ↗ Hereditary colorectal cancer syndromes: American Society of Clinical Oncology Clinical Practice Guideline endorsement of the familial risk-colorectal cancer: European Society for Medical Oncology Clinical Practice Guidelines. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR