APBA1 p.Ser347=
c.1041G>A · rs150860646 · VCV713715
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.776%, 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 -1.1 | GERP -5, phastCons 0.001 |
| Overall | ||
| CADD | 9.467 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.776%
African / African-American · 580/74,768 alleles
Filtering AF
0.724%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.703%
Overall
0.0414%
667/1,610,844 alleles · rare
exomes 317/1,458,938 · genomes 350/151,906 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.776% | 129 |
| Remaining individualsnot grpmax-eligible | 0.069% | 1,450 |
| Admixed American | 0.0468% | 2,137 |
| South Asian | 0.0022% | 45,452 |
| Finnishnot grpmax-eligible | 0.00157% | 63,524 |
| European (non-Finnish) | 0.0011% | 90,655 |
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
- APBA1
- Protein
- p.Ser347=
- Coding
- c.1041G>A
- MANE Select
- NM_001163
- dbSNP
- rs150860646
- Type
- single nucleotide variant
- Location
- chr9:69516170 (GRCh38)
- Gene constraint
- LOEUF 0.978 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.85 · 8 PDB
Similar variants
- APBA1 p.Asn810Ser Uncertain significance ★★ ⚠ same type
- APBA1 p.Ala225Val Uncertain significance ★ ⚠ same type
- APBA1 p.Ala329Val Uncertain significance ★ ⚠ same type
- APBA1 p.Ala345Thr Uncertain significance ★ ⚠ same type
- APBA1 p.Ala506Pro Uncertain significance ★ ⚠ same type
- APBA1 p.Ala574Val Uncertain significance ★ ⚠ same type
- APBA1 p.Arg143Cys Uncertain significance ★ ⚠ same type
- APBA1 p.Arg177His Uncertain significance ★ ⚠ 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/apba1-p-ser347 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown