Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.23%, afr)
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 -5.4 | GERP -3.5 |
| Overall | ||
| CADD | 0.244 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.23%
African / African-American · 926/75,012 alleles
Filtering AF
1.17%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.14%
Overall
0.064%
1,033/1,614,028 alleles · low-frequency
exomes 508/1,461,792 · genomes 525/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.23% | 81 |
| Remaining individualsnot grpmax-eligible | 0.0704% | 1,420 |
| Admixed American | 0.0533% | 1,875 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.0132% | 7,588 |
| European (non-Finnish) | 0.00153% | 65,554 |
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
- AKAP1
- Protein
- p.Thr850=
- Coding
- c.2550G>A
- MANE Select
- NM_003488
- dbSNP
- rs2230769
- Type
- single nucleotide variant
- Location
- chr17:57118430 (GRCh38)
- Gene constraint
- LOEUF 0.526 · pLI 0.67 (gnomAD)
- Structure
- AlphaFold pLDDT 57.02
Similar variants
- AKAP1 p.Thr850Met Uncertain significance ★ same residue
- AKAP1 c.1976-6A>G Benign ★★ same type
- AKAP1 p.Ala218Thr Benign ★★ same type
- AKAP1 p.Gly323Ser Benign ★★ same type
- AKAP1 p.Pro475= Benign ★★ same type
- AKAP1 p.Pro818= Benign ★★ same type
- AKAP1 p.Ser330Gly Benign ★★ same type
- AKAP1 p.Ser388= Benign ★★ 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/akap1-p-thr850 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown