APBA2 p.Ile101=
c.303C>T · rs142673699 · VCV790687
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.505%, 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 0.97 | GERP -0.9, phastCons 1 |
| Overall | ||
| CADD | 9.897 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.505%
African / African-American · 379/75,056 alleles
Filtering AF
0.463%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.447%
Overall
0.0271%
437/1,614,204 alleles · rare
exomes 203/1,461,880 · genomes 234/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.505% | 198 |
| Admixed American | 0.0366% | 2,729 |
| Middle Eastern | 0.033% | 3,031 |
| Remaining individualsnot grpmax-eligible | 0.032% | 3,125 |
| East Asian | 0.00446% | 22,437 |
| European (non-Finnish) | 0.00102% | 98,336 |
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
- APBA2
- Protein
- p.Ile101=
- Coding
- c.303C>T
- MANE Select
- NM_001353788
- dbSNP
- rs142673699
- Type
- single nucleotide variant
- Location
- chr15:29054187 (GRCh38)
- Gene constraint
- LOEUF 0.524 · pLI 0.78 (gnomAD)
- Structure
- AlphaFold pLDDT 59.74
Similar variants
- APBA2 p.Val77Met Uncertain significance ★★ ⚠ same type
- APBA2 c.1216-9T>C Benign ★★ same type
- APBA2 c.1525-8C>G Likely benign ★★ same type
- APBA2 c.1705-9C>T Benign ★★ same type
- APBA2 p.Asp87= Benign ★★ same type
- APBA2 p.Gly206= Benign ★★ same type
- APBA2 p.His127= Benign ★★ same type
- APBA2 p.Ile512= 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/apba2-p-ile101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown