AGO3 p.Phe747=
c.2241C>T · rs145947091 · VCV3052619
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.317%, afr)
Conditions
1
AGO3-related disorder
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 2.8 | GERP 0.92, phastCons 1 |
| Overall | ||
| CADD | 12.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.317%
African / African-American · 238/74,998 alleles
Filtering AF
0.284%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.271%
Overall
0.0514%
829/1,613,432 alleles · rare
exomes 658/1,461,166 · genomes 171/152,266 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.317% | 315 |
| Admixed American | 0.0467% | 2,139 |
| Remaining individualsnot grpmax-eligible | 0.0432% | 2,314 |
| European (non-Finnish) | 0.0425% | 2,355 |
| South Asian | 0.0352% | 2,842 |
| Middle Eastern | 0.0165% | 6,058 |
| Finnishnot grpmax-eligible | 0.00312% | 32,010 |
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
- AGO3
- Protein
- p.Phe747=
- Coding
- c.2241C>T
- MANE Select
- NM_024852
- dbSNP
- rs145947091
- Type
- single nucleotide variant
- Location
- chr1:36043515 (GRCh38)
- Gene constraint
- LOEUF 0.232 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 91.93 · 2 PDB
- Residue 747
- the piwi domain; a β-strand
Disease context
AGO3-related disorder
Similar variants
- AGO3 p.Arg426Gln Uncertain significance ★ ⚠ same condition
- AGO3 p.Thr338Ile Uncertain significance ★ ⚠ same condition
- AGO3 p.Ala597= Likely benign same condition
- AGO3 p.Gln709= Likely benign same condition
- AGO3 p.His191= Likely benign same condition
- AGO3 p.Pro324= Likely benign same condition
- AGO3 p.Arg403= Benign/Likely benign ★★ same type
- AGO3 p.Gln781= 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/ago3-p-phe747 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown