Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Common
common (popmax 92.5%, 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 -12 | GERP -3.5 |
| Overall | ||
| CADD | 0.772 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
92.5%
African / African-American · 69,378/74,970 alleles
Filtering AF
92%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 91.7%
Overall
81.9%
1,321,719/1,613,966 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 92.5% | 1 |
| Admixed American | 89.3% | 1 |
| Finnishnot grpmax-eligible | 84.3% | 1 |
| East Asian | 83.3% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 82% | 1 |
| South Asian | 81.9% | 1 |
| Remaining individualsnot grpmax-eligible | 81.7% | 1 |
| European (non-Finnish) | 80.7% | 1 |
| Amishnot grpmax-eligible | 76.4% | 1 |
| Middle Eastern | 75.9% | 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
- APOL1
- Protein
- p.Arg320=
- Coding
- c.960G>A
- MANE Select
- NM_003661
- dbSNP
- rs136177
- Type
- single nucleotide variant
- Location
- chr22:36265796 (GRCh38)
- Gene constraint
- LOEUF 1.68 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.94 · 5 PDB
Similar variants
- APOL1 p.Ala108Glu Uncertain significance ★★ ⚠ same type
- APOL1 p.Ala394Gly Uncertain significance ★★ ⚠ same type
- APOL1 p.Arg112Cys Uncertain significance ★★ ⚠ same type
- APOL1 p.Asp46Gly Uncertain significance ★★ ⚠ same type
- APOL1 p.Gln396Ter Uncertain significance ★★ same type
- APOL1 p.Glu110Asp Uncertain significance ★★ ⚠ same type
- APOL1 p.Glu323Gln Uncertain significance ★★ ⚠ same type
- APOL1 p.His298Arg 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/apol1-p-arg320 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown