ATG9A p.His161=
c.483C>T · rs191487005 · VCV730112
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.603%, 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 3.4 | GERP -0.11, phastCons 1 |
| Overall | ||
| CADD | 6.83 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.603%
African / African-American · 453/75,072 alleles
Filtering AF
0.557%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.539%
Overall
0.031%
500/1,614,218 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.603% | 166 |
| Remaining individualsnot grpmax-eligible | 0.0256% | 3,907 |
| Admixed American | 0.025% | 4,002 |
| European (non-Finnish) | 0.00136% | 73,753 |
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
- ATG9A
- Protein
- p.His161=
- Coding
- c.483C>T
- MANE Select
- NM_001077198
- dbSNP
- rs191487005
- Type
- single nucleotide variant
- Location
- chr2:219225104 (GRCh38)
- Gene constraint
- LOEUF 0.333 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.84 · 8 PDB
- Residue 161
- an α-helix
Similar variants
- ATG9A c.1266-5A>G Benign ★★ same type
- ATG9A p.Ala115Thr Uncertain significance ★ ⚠ same type
- ATG9A p.Ala2Thr Uncertain significance ★ ⚠ same type
- ATG9A p.Ala30Thr Uncertain significance ★ ⚠ same type
- ATG9A p.Ala326Thr Uncertain significance ★ ⚠ same type
- ATG9A p.Ala389Pro Uncertain significance ★ ⚠ same type
- ATG9A p.Ala443Thr Uncertain significance ★ ⚠ same type
- ATG9A p.Ala589Val 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/atg9a-p-his161 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown