APBA2 p.Ser11=
c.33C>T · rs116221298 · VCV715862
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.27%, 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 2.6 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 12.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.27%
African / African-American · 1,698/74,896 alleles
Filtering AF
2.18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.14%
Overall
0.119%
1,925/1,612,646 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.27% | 44 |
| Middle Eastern | 0.116% | 865 |
| Remaining individualsnot grpmax-eligible | 0.104% | 960 |
| Admixed American | 0.0801% | 1,249 |
| South Asian | 0.0121% | 8,273 |
| European (non-Finnish) | 0.00797% | 12,543 |
| East Asian | 0.00447% | 22,385 |
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.Ser11=
- Coding
- c.33C>T
- MANE Select
- NM_001353788
- dbSNP
- rs116221298
- Type
- single nucleotide variant
- Location
- chr15:29053917 (GRCh38)
- Gene constraint
- LOEUF 0.524 · pLI 0.78 (gnomAD)
- Structure
- AlphaFold pLDDT 59.74
- Residue 11
- a modified residue (phosphoserine); the 'disordered' region
Similar variants
- APBA2 p.Ser11Asn Uncertain significance ★ ⚠ same residue
- 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
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-ser11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown