ABCA1 p.Ala1010=
c.3030G>A · rs561878562 · VCV1799041
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
Conditions
1
Cardiovascular phenotype
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 -8.6 | GERP -4.2 |
| Overall | ||
| CADD | 0.527 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/60,016 alleles
Filtering AF
0.00223%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00198%
Overall
0.0026%
42/1,614,090 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 20,005 |
| European (non-Finnish) | 0.00305% | 32,778 |
| East Asian | 0.00223% | 44,880 |
| African / African-American | 0.00133% | 75,022 |
| South Asian | 0.0011% | 91,078 |
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
- ABCA1
- Protein
- p.Ala1010=
- Coding
- c.3030G>A
- MANE Select
- NM_005502
- dbSNP
- rs561878562
- Type
- single nucleotide variant
- Location
- chr9:104820000 (GRCh38)
- Gene constraint
- LOEUF 0.563 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.50 · 7 PDB
- Residue 1010
- the abc transporter 1 domain; an α-helix
Similar variants
- ABCA1 p.Ala1010Val Likely benign ★ same residue
- ABCA1 c.4175+1G>T Pathogenic/Likely pathogenic ★★ same condition
- ABCA1 p.Thr940Met Pathogenic/Likely pathogenic ★★ same condition
- ABCA1 c.3787+5C>A Uncertain significance ★★ same condition
- ABCA1 p.Ala1855Ser Uncertain significance ★★ ⚠ same condition
- ABCA1 p.Ala766Ser Uncertain significance ★★ ⚠ same condition
- ABCA1 p.Arg1283Cys Uncertain significance ★★ ⚠ same condition
- ABCA1 p.Arg1342Trp Uncertain significance ★★ ⚠ 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/abca1-p-ala1010 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown