Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.21%, 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 0.44 | GERP -1.5 |
| Overall | ||
| CADD | 1.699 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.21%
Middle Eastern · 69/5,696 alleles
Filtering AF
0.982%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.898%
Overall
0.146%
2,340/1,600,040 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.21% | 83 |
| Admixed American | 0.666% | 150 |
| African / African-American | 0.424% | 236 |
| Remaining individualsnot grpmax-eligible | 0.32% | 312 |
| European (non-Finnish) | 0.113% | 884 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0547% | 1,827 |
| South Asian | 0.0292% | 3,424 |
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.Cys786=
- Coding
- c.2358C>T
- MANE Select
- NM_019112
- dbSNP
- rs9282560
- Type
- single nucleotide variant
- Location
- chr19:1048983 (GRCh38)
- Gene constraint
- LOEUF 1.368 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.77 · 6 PDB
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-cys786 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown