AGO2 p.Ala643=
c.1929C>T · rs113224509 · VCV709067
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.75%, 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 -6.2 | GERP -3.8 |
| Overall | ||
| CADD | 2.231 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.75%
African / African-American · 1,313/75,070 alleles
Filtering AF
1.67%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.64%
Overall
0.0938%
1,513/1,613,586 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.75% | 57 |
| Remaining individualsnot grpmax-eligible | 0.131% | 762 |
| Admixed American | 0.117% | 857 |
| Middle Eastern | 0.0825% | 1,212 |
| South Asian | 0.0154% | 6,497 |
| European (non-Finnish) | 0.00246% | 40,686 |
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
- AGO2
- Protein
- p.Ala643=
- Coding
- c.1929C>T
- MANE Select
- NM_012154
- dbSNP
- rs113224509
- Type
- single nucleotide variant
- Location
- chr8:140541269 (GRCh38)
- Gene constraint
- LOEUF 0.102 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 92.82 · 71 PDB
- Residue 643
- an α-helix; the piwi domain
Similar variants
- AGO2 p.Arg714Trp Pathogenic/Likely pathogenic ★★ same type
- AGO2 p.Cys751Tyr Pathogenic/Likely pathogenic ★★ same type
- AGO2 p.Gly201Val Pathogenic/Likely pathogenic ★★ same type
- AGO2 p.Gly604Arg Pathogenic/Likely pathogenic ★★ same type
- AGO2 p.Thr357Met Pathogenic/Likely pathogenic ★★ same type
- AGO2 p.Ala142Thr Uncertain significance ★★ ⚠ same type
- AGO2 p.Ala372Val Uncertain significance ★★ ⚠ same type
- AGO2 p.Arg630His 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/ago2-p-ala643 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown