Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 12 submitters
gnomAD v4.1
Common
common (popmax 76.5%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
1
acyl-CoA dehydrogenase 9 deficiency
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 2.7 | GERP 0.59, phastCons 0.99 |
| Overall | ||
| CADD | 10.16 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
76.5%
African / African-American · 57,202/74,804 alleles
Filtering AF
75.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 75.7%
Overall
34%
547,563/1,611,358 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 76.5% | 1 |
| East Asian | 62.2% | 2 |
| Admixed American | 43.7% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 41.3% | 2 |
| South Asian | 37.2% | 3 |
| Remaining individualsnot grpmax-eligible | 36.2% | 3 |
| Middle Eastern | 36% | 3 |
| European (non-Finnish) | 29.5% | 3 |
| Finnishnot grpmax-eligible | 28.2% | 4 |
| Amishnot grpmax-eligible | 20.9% | 5 |
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
- ACAD9
- Protein
- p.Arg127=
- Coding
- c.379A>C
- MANE Select
- NM_014049
- dbSNP
- rs1680778
- Type
- single nucleotide variant
- Location
- chr3:128895342 (GRCh38)
- Gene constraint
- LOEUF 0.884 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.09 · 2 PDB
- Residue 127
- an α-helix; a UniProt-annotated variant site (in mc1dn20)
Disease context
acyl-CoA dehydrogenase 9 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Acyl-CoA dehydrogenase 9 deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood, Infancy, Neonatal
Similar variants
- ACAD9 p.Arg127Ter Likely pathogenic ★ same residue
- ACAD9 c.1150-2A>G Likely pathogenic ★★ same condition
- ACAD9 c.1278+1G>T Likely pathogenic ★★ same condition
- ACAD9 c.1279-2A>C Likely pathogenic ★★ same condition
- ACAD9 c.1358+2T>G Likely pathogenic ★★ same condition
- ACAD9 c.1359-1G>A Pathogenic/Likely pathogenic ★★ same condition
- ACAD9 c.1563+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ACAD9 c.1A>G Pathogenic/Likely pathogenic ★★ same condition
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/acad9-p-arg127 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown