ACACA p.Asn990=
c.2970C>T · rs867660985 · VCV3042828
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.363%, mid)
Conditions
1
ACACA-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 3 | GERP -2.2, phastCons 1 |
| Overall | ||
| CADD | 7.977 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.363%
Middle Eastern · 22/6,062 alleles
Filtering AF
0.246%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.207%
Overall
0.0015%
22/1,461,848 alleles · rare
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
- ACACA
- Protein
- p.Asn990=
- Coding
- c.2970C>T
- MANE Select
- NM_198834
- dbSNP
- rs867660985
- Type
- single nucleotide variant
- Location
- chr17:37242015 (GRCh38)
- Gene constraint
- LOEUF 0.374 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 83.05 · 10 PDB
- Residue 990
- an α-helix
Disease context
ACACA-related disorder
Similar variants
- ACACA c.5569-10C>G Likely benign same condition
- ACACA p.Leu1734= Likely benign same condition
- ACACA p.Ser789= Likely benign same condition
- ACACA p.Val2008= Likely benign same condition
- ACACA p.Pro699fs Uncertain significance same condition
- ACACA c.4777-8del Likely benign same condition
- ACACA p.Ala2308Val Uncertain significance ★★ ⚠ same type
- ACACA p.Arg1206His 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/acaca-p-asn990 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown