Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.815%, eas)
Conditions
1
platelet-type bleeding disorder 9
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.69 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.35 | gain · loss 0.18 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.3 | GERP 0.75, phastCons 1 |
| Overall | ||
| CADD | 20.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.815%
East Asian · 365/44,784 alleles
Filtering AF
0.746%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.719%
Overall
0.0278%
449/1,613,026 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.815% | 123 |
| Remaining individualsnot grpmax-eligible | 0.0656% | 1,523 |
| South Asian | 0.0132% | 7,588 |
| Admixed American | 0.00333% | 29,986 |
| African / African-American | 0.00267% | 37,489 |
| European (non-Finnish) | 0.00229% | 43,675 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- ITGA2
- Protein
- p.Val211=
- Coding
- c.633G>A
- MANE Select
- NM_002203
- dbSNP
- rs26675
- Type
- single nucleotide variant
- Location
- chr5:53051413 (GRCh38)
- Gene constraint
- LOEUF 0.789 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.80 · 23 PDB
- Residue 211
- a β-strand; the vwfa domain
Similar variants
- ITGA2 p.Asn57Lys Uncertain significance ★★ ⚠ same condition
- ITGA2 p.Gln690Arg Uncertain significance ★★ ⚠ same condition
- ITGA2 p.Gly201Asp Uncertain significance ★★ ⚠ same condition
- ITGA2 p.Gly205Val Uncertain significance ★★ ⚠ same condition
- ITGA2 c.1312+12T>C Benign/Likely benign ★★ same condition
- ITGA2 c.1807-6T>C Benign/Likely benign ★★ same condition
- ITGA2 c.2236-62T>C Benign ★★ same condition
- ITGA2 c.2742-4A>G Benign/Likely benign ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/itga2-p-val211 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown