ABCA7 p.Ala689=
c.2067G>A · rs200288020 · VCV3043653
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.292%, afr)
Conditions
1
ABCA7-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.74 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.51 | loss · gain 0.09 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP 0.48, phastCons 1 |
| Overall | ||
| CADD | 19.12 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.292%
African / African-American · 215/73,642 alleles
Filtering AF
0.26%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.248%
Overall
0.0182%
285/1,564,774 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.292% | 343 |
| Remaining individualsnot grpmax-eligible | 0.0264% | 3,789 |
| Admixed American | 0.0168% | 5,950 |
| European (non-Finnish) | 0.00379% | 26,409 |
| Finnishnot grpmax-eligible | 0.00205% | 48,822 |
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
- ABCA7
- Protein
- p.Ala689=
- Coding
- c.2067G>A
- MANE Select
- NM_019112
- dbSNP
- rs200288020
- Type
- single nucleotide variant
- Location
- chr19:1047378 (GRCh38)
- Gene constraint
- LOEUF 1.368 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.77 · 6 PDB
- Residue 689
- a β-strand
Disease context
ABCA7-related disorder
Similar variants
- ABCA7 c.4417-1G>C Likely pathogenic ★ same condition
- ABCA7 p.Gln1083Ter Pathogenic ★ same condition
- ABCA7 p.Arg1754Ter Likely pathogenic same condition
- ABCA7 p.Glu269Ter Likely pathogenic same condition
- ABCA7 c.790+10T>G Benign same condition
- ABCA7 c.-9A>G Benign same condition
- ABCA7 p.Ala1441= Likely benign same condition
- ABCA7 p.Ala1864= Benign 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/abca7-p-ala689 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown