ITGA2 p.Ser20=
c.60T>C · VCV4970316
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.383%, afr)
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 -0.19 | GERP -4.4, phastCons 0.003 |
| Overall | ||
| CADD | 7.979 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.383%
African / African-American · 287/75,006 alleles
Filtering AF
0.346%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.332%
Overall
0.0196%
317/1,613,948 alleles · rare
exomes 154/1,461,850 · genomes 163/152,098 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.383% | 261 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,167 |
| Admixed American | 0.0233% | 4,286 |
| European (non-Finnish) | 8.47e-05% | 1,179,958 |
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.Ser20=
- Coding
- c.60T>C
- MANE Select
- NM_002203
- Type
- single nucleotide variant
- Location
- chr5:52989528 (GRCh38)
- Gene constraint
- LOEUF 0.789 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.80 · 23 PDB
Similar variants
- ITGA2 p.Asn57Lys Uncertain significance ★★ ⚠ same type
- ITGA2 p.Gln690Arg Uncertain significance ★★ ⚠ same type
- ITGA2 p.Gly201Asp Uncertain significance ★★ ⚠ same type
- ITGA2 p.Gly205Val Uncertain significance ★★ ⚠ same type
- ITGA2 c.1173+172A>T Benign ★★ same type
- ITGA2 c.1312+12T>C Benign/Likely benign ★★ same type
- ITGA2 c.1313-30T>G Benign ★★ same type
- ITGA2 c.1313-39T>C Benign ★★ same type
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-ser20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown