AGAP1 p.Ala805=
c.2415T>G · rs11895915 · VCV2114467
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 64.5%, 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. | ||
| REVEL | 0.096 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -5.5 | GERP -3.4 |
| Overall | ||
| CADD | 4.099 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
64.5%
African / African-American · 48,279/74,844 alleles
Filtering AF
64%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 63.8%
Overall
27.9%
449,629/1,613,248 alleles · common
exomes 394,940/1,461,558 · genomes 54,689/151,690 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 64.5% | 2 |
| South Asian | 36.4% | 3 |
| Finnishnot grpmax-eligible | 29.6% | 3 |
| Remaining individualsnot grpmax-eligible | 28.4% | 4 |
| Middle Eastern | 26.7% | 4 |
| European (non-Finnish) | 26% | 4 |
| Amishnot grpmax-eligible | 23.1% | 4 |
| East Asian | 20.1% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 18.2% | 5 |
| Admixed American | 14.5% | 7 |
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.Ala805=
- Coding
- c.2415T>G
- MANE Select
- NM_001037131
- dbSNP
- rs11895915
- Type
- single nucleotide variant
- Location
- chr2:236123963 (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-ala805 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown