Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.926%, 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 -1.7 | GERP -2.5 |
| Overall | ||
| CADD | 6.982 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.926%
African / African-American · 691/74,658 alleles
Filtering AF
0.868%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.846%
Overall
0.19%
3,058/1,610,430 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.926% | 108 |
| Ashkenazi Jewishnot grpmax-eligible | 0.615% | 163 |
| Finnishnot grpmax-eligible | 0.347% | 288 |
| Admixed American | 0.26% | 384 |
| Middle Eastern | 0.248% | 403 |
| Remaining individualsnot grpmax-eligible | 0.234% | 427 |
| European (non-Finnish) | 0.135% | 738 |
| South Asian | 0.0395% | 2,529 |
| East Asian | 0.0357% | 2,804 |
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
- AOC3
- Protein
- p.Tyr271=
- Coding
- c.813C>T
- MANE Select
- NM_003734
- dbSNP
- rs448383
- Type
- single nucleotide variant
- Location
- chr17:42852156 (GRCh38)
- Gene constraint
- LOEUF 1.056 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.15 · 11 PDB
- Residue 271
- a β-strand
Similar variants
- AOC3 p.Arg73Cys Uncertain significance ★★ ⚠ same type
- AOC3 p.Ala582Thr Benign ★★ same type
- AOC3 p.Arg329Gln Benign/Likely benign ★★ same type
- AOC3 p.Arg441Trp Benign ★★ ⚠ same type
- AOC3 p.Arg566Gln Likely benign ★★ same type
- AOC3 p.Ile371Thr Benign ★★ same type
- AOC3 p.Tyr406Asn Benign ★★ ⚠ same type
- AOC3 p.Ala124Thr 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/aoc3-p-tyr271 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown