AGAP1 p.Asp794=
c.2382C>T · rs73996547 · VCV779327
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 5.28%, 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. | ||
| REVEL | 0.242 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.8 | GERP -3.4 |
| Overall | ||
| CADD | 8.677 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.28%
African / African-American · 3,958/74,984 alleles
Filtering AF
5.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.09%
Overall
0.395%
6,367/1,613,022 alleles · common
exomes 3,899/1,460,774 · genomes 2,468/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.28% | 19 |
| Middle Eastern | 2.38% | 42 |
| Admixed American | 0.792% | 126 |
| Remaining individualsnot grpmax-eligible | 0.695% | 144 |
| European (non-Finnish) | 0.111% | 901 |
| Ashkenazi Jewishnot grpmax-eligible | 0.108% | 925 |
| South Asian | 0.0297% | 3,371 |
| Finnishnot grpmax-eligible | 0.00156% | 63,910 |
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
- AGAP1
- Protein
- p.Asp794=
- Coding
- c.2382C>T
- MANE Select
- NM_001037131
- dbSNP
- rs73996547
- Type
- single nucleotide variant
- Location
- chr2:236123930 (GRCh38)
- Gene constraint
- LOEUF 0.366 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.01 · 2 PDB
Similar variants
- AGAP1 p.Ala418Ser Uncertain significance ★★ ⚠ same type
- AGAP1 p.Ala52Ser Uncertain significance ★★ ⚠ same type
- AGAP1 p.Ala570Gly Uncertain significance ★★ same type
- AGAP1 p.Ala809Ser Uncertain significance ★★ ⚠ same type
- AGAP1 p.Arg14Trp Uncertain significance ★★ ⚠ same type
- AGAP1 p.Arg313His Uncertain significance ★★ ⚠ same type
- AGAP1 p.Arg696Trp Uncertain significance ★★ ⚠ same type
- AGAP1 p.Arg770Cys 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/agap1-p-asp794 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown