ABCA7 p.Glu1679=
c.5037G>A · rs115536223 · VCV444441
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.867%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.033 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.36 | donor loss · deltas |
| Constraint at this position | ||
| Conservation | phyloP -0.75 | GERP -3.7, phastCons 0.001 |
| Overall | ||
| CADD | 0.789 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.867%
African / African-American · 650/75,006 alleles
Filtering AF
0.811%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.789%
Overall
0.0468%
755/1,613,924 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.867% | 115 |
| Remaining individualsnot grpmax-eligible | 0.0896% | 1,116 |
| Admixed American | 0.0667% | 1,500 |
| Middle Eastern | 0.033% | 3,031 |
| South Asian | 0.00329% | 30,358 |
| European (non-Finnish) | 0.000339% | 294,998 |
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.Glu1679=
- Coding
- c.5037G>A
- MANE Select
- NM_019112
- dbSNP
- rs115536223
- Type
- single nucleotide variant
- Location
- chr19:1058157 (GRCh38)
- Gene constraint
- LOEUF 1.368 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.77 · 6 PDB
- Residue 1679
- an α-helix
Similar variants
- ABCA7 p.Glu1679Ter Likely pathogenic ★ same residue
- 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
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-glu1679 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown