Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Common
common (popmax 100%, eas) — 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. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -3.8 |
| Overall | ||
| CADD | 0.973 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
100%
East Asian · 44,860/44,872 alleles
Filtering AF
99.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 98.9%
Overall
84.4%
1,362,344/1,613,950 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 100% | 1 |
| South Asian | 96.5% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 94.2% | 1 |
| Middle Eastern | 92.9% | 1 |
| Admixed American | 91.9% | 1 |
| Amishnot grpmax-eligible | 91.1% | 1 |
| Remaining individualsnot grpmax-eligible | 86% | 1 |
| Finnishnot grpmax-eligible | 83% | 1 |
| European (non-Finnish) | 82.9% | 1 |
| African / African-American | 72.7% | 1 |
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
- A2ML1
- Protein
- p.Pro789=
- Coding
- c.2367G>A
- MANE Select
- NM_144670
- dbSNP
- rs1860927
- Type
- single nucleotide variant
- Location
- chr12:8851916 (GRCh38)
- Gene constraint
- LOEUF 0.953 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.61 · 5 PDB
- Residue 789
- a β-strand; a UniProt-annotated variant site (risk factor for otitis media)
Similar variants
- A2ML1 p.Pro789Leu Uncertain significance ★ ⚠ same residue
- A2ML1 c.1834-1G>T Uncertain significance ★★ same type
- A2ML1 c.3264+4C>T Uncertain significance ★★ same type
- A2ML1 c.3933+4A>G Uncertain significance ★★ same type
- A2ML1 c.409+1G>A Uncertain significance ★★ same type
- A2ML1 c.4221+2T>C Uncertain significance ★★ same type
- A2ML1 c.*1+1G>A Uncertain significance ★★ same type
- A2ML1 p.Ala1002Val 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/a2ml1-p-pro789 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown