ITGA2B p.Val616=
c.1848G>A · rs79289329 · VCV323550
ClinGen expert panel — Platelet Disorders VCEP
Benign for Glanzmann's thrombasthenia. Applied ACMG criteria (verbatim):
BP7 BP4 BA1
Curation rationale (ClinGen, verbatim)
The c.1848G>A (p.Val616=) synonymous variant has not been reported in the literature to our knowledge. It is present in the gnomAD African population at an allele frequency of 0.01899. No splice impact is predicted and the variant is not highly conserved. In summary, this variant meets criteria to be classified as benign for GT. GT-specific criteria applied: BA1, BP4, and BP7.
ClinGen Evidence Repository → · reported verbatim, not re-tallied by Sugi Variant.
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 0.79 | GERP 0.29, phastCons 1 |
| Overall | ||
| CADD | 10.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.8% | 56 |
| Admixed American | 0.223% | 448 |
| Middle Eastern | 0.198% | 505 |
| Remaining individualsnot grpmax-eligible | 0.157% | 638 |
| European (non-Finnish) | 0.00661% | 15,129 |
| South Asian | 0.00329% | 30,361 |
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
- ITGA2B
- Protein
- p.Val616=
- Coding
- c.1848G>A
- MANE Select
- NM_000419
- dbSNP
- rs79289329
- Type
- single nucleotide variant
- Location
- chr17:44379719 (GRCh38)
- Gene constraint
- LOEUF 0.763 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.00 · 80 PDB
- Residue 616
- a β-strand
Disease context
Glanzmann thrombasthenia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Glanzmann thrombasthenia (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- ITGA2B p.Val616Met Benign/Likely benign ★★ same residue
- ITGA2B c.1210+105A>G Likely pathogenic ★★★ same condition
- ITGA2B c.1210+5G>A Likely pathogenic ★★★ same condition
- ITGA2B c.1211-1G>C Likely pathogenic ★★★ same condition
- ITGA2B c.1544+1G>A Pathogenic ★★★ same condition
- ITGA2B c.1545-1G>A Pathogenic ★★★ same condition
- ITGA2B c.1600+1G>A Pathogenic ★★★ same condition
- ITGA2B c.1752+2T>C Pathogenic ★★★ 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/itga2b-p-val616 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown