Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 16.8%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
1
platelet-type bleeding disorder 9
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.091 | GERP -4.3, phastCons 0.86 |
| Overall | ||
| CADD | 8.618 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
16.8%
African / African-American · 12,565/74,908 alleles
Filtering AF
16.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 16.4%
Overall
8.95%
144,290/1,612,506 alleles · common
exomes 128,259/1,460,350 · genomes 16,031/152,156 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 16.8% | 6 |
| Middle Eastern | 15.6% | 6 |
| Ashkenazi Jewishnot grpmax-eligible | 11.5% | 9 |
| South Asian | 9.74% | 10 |
| Remaining individualsnot grpmax-eligible | 9.56% | 10 |
| European (non-Finnish) | 8.8% | 11 |
| Admixed American | 6.41% | 16 |
| Finnishnot grpmax-eligible | 5.32% | 19 |
| Amishnot grpmax-eligible | 3.84% | 26 |
| East Asian | 3.31% | 30 |
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.Ala263=
- Coding
- c.789T>C
- MANE Select
- NM_002203
- dbSNP
- rs1139484
- Type
- single nucleotide variant
- Location
- chr5:53055547 (GRCh38)
- Gene constraint
- LOEUF 0.789 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.80 · 23 PDB
- Residue 263
- an α-helix; 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-ala263 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown