ABCA7 p.Pro2009=
c.6027G>A · rs538148125 · VCV3046767
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0352%, mid)
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 -3.1 | GERP -3.7 |
| Overall | ||
| CADD | 5.188 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0352%
Middle Eastern · 2/5,676 alleles
Filtering AF
0.00618%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00255%
Overall
0.00141%
22/1,565,212 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0352% | 2,838 |
| Remaining individualsnot grpmax-eligible | 0.0033% | 30,319 |
| South Asian | 0.00235% | 42,621 |
| Admixed American | 0.00189% | 53,050 |
| European (non-Finnish) | 0.0013% | 77,105 |
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.Pro2009=
- Coding
- c.6027G>A
- MANE Select
- NM_019112
- dbSNP
- rs538148125
- Type
- single nucleotide variant
- Location
- chr19:1064236 (GRCh38)
- Gene constraint
- LOEUF 1.368 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.77 · 6 PDB
- Residue 2009
- the abc transporter 2 domain; an α-helix
Similar variants
- ABCA7 c.2684+5G>A Uncertain significance ★★ same type
- ABCA7 c.3578-2A>G Uncertain significance ★★ same type
- ABCA7 p.Arg1026Cys Uncertain significance ★★ ⚠ same type
- ABCA7 p.Arg652Cys Uncertain significance ★★ ⚠ same type
- ABCA7 p.Arg880Trp Uncertain significance ★★ ⚠ same type
- ABCA7 p.Asp1452Asn Uncertain significance ★★ ⚠ same type
- ABCA7 p.Asp2085Asn Uncertain significance ★★ ⚠ same type
- ABCA7 p.Gln925Ter 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/abca7-p-pro2009 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown