ACACA c.338+16A>G
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.506%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +16 | near-intronic (+16 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.82 | GERP -3.7 |
| Non-coding constraint | Z 1.47 | 1 kb window · o/e 0.88 · regional · uncalibrated |
| Overall | ||
| CADD | 7.018 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.506%
African / African-American · 380/75,042 alleles
Filtering AF
0.464%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.448%
Overall
0.0291%
470/1,613,886 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.506% | 197 |
| Middle Eastern | 0.115% | 866 |
| Remaining individualsnot grpmax-eligible | 0.048% | 2,083 |
| Admixed American | 0.0267% | 3,751 |
| South Asian | 0.00769% | 13,011 |
| East Asian | 0.00669% | 14,956 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,596 |
| European (non-Finnish) | 0.00212% | 47,195 |
| Finnishnot grpmax-eligible | 0.00156% | 63,936 |
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
- Coding
- c.338+16A>G
- MANE Select
- NM_198834
- dbSNP
- rs143267096
- Type
- single nucleotide variant
- Location
- chr17:37330157 (GRCh38)
- Gene constraint
- LOEUF 0.374 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 83.05 · 10 PDB
Similar variants
- ACACA p.Ala2308Val Uncertain significance ★★ ⚠ same type
- ACACA p.Arg1206His Uncertain significance ★★ ⚠ same type
- ACACA p.Arg2198Gln Uncertain significance ★★ ⚠ same type
- ACACA p.Arg745Trp Uncertain significance ★★ ⚠ same type
- ACACA p.Asn1903Ser Uncertain significance ★★ ⚠ same type
- ACACA p.Asn728Ser Uncertain significance ★★ ⚠ same type
- ACACA p.Asn950Ser Uncertain significance ★★ ⚠ same type
- ACACA p.Asp2228Asn 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-c-338-plus-16a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown