ABCA2 p.Ala20=
c.60T>C · rs4880189 · VCV1249256
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 84.1%, afr) — too common for a highly-penetrant pathogenic allele
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 -0.29 | GERP -0.93 |
| Overall | ||
| CADD | 7.811 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
84.1%
African / African-American · 52,503/62,434 alleles
Filtering AF
83.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 83.2%
Overall
72.9%
944,154/1,295,756 alleles · common
exomes 828,870/1,143,574 · genomes 115,284/152,182 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 84.1% | 1 |
| East Asian | 76% | 1 |
| South Asian | 75.7% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 75.5% | 1 |
| Admixed American | 73.5% | 1 |
| Remaining individualsnot grpmax-eligible | 73% | 1 |
| European (non-Finnish) | 72% | 1 |
| Amishnot grpmax-eligible | 71.8% | 1 |
| Finnishnot grpmax-eligible | 69.7% | 1 |
| Middle Eastern | 68.4% | 1 |
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
- ABCA2
- Protein
- p.Ala20=
- Coding
- c.60T>C
- MANE Select
- NM_001606 · reported on NM_212533
- dbSNP
- rs4880189
- Type
- single nucleotide variant
- Location
- chr9:137028813 (GRCh38)
- Gene constraint
- LOEUF 0.436 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.46
Similar variants
- ABCA2 p.Gln1370Ter Likely pathogenic ★★ same type
- ABCA2 c.3883-3C>T Uncertain significance ★★ same type
- ABCA2 p.Ala1357Thr Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala1620Thr Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala1645Val Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala1715Ser Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala2180Thr Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala2206Val 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/abca2-p-ala20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown