ACAA2 c.16+17C>T
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.26%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +17 | near-intronic (+17 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.05 | GERP -3.3 |
| Non-coding constraint | Z 1.63 | 1 kb window · o/e 0.91 · regional · uncalibrated |
| Overall | ||
| CADD | 9.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.26%
European (non-Finnish) · 22,326/987,532 alleles
Filtering AF
2.24%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.23%
Overall
2%
24,778/1,241,872 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 2.26% | 44 |
| Finnishnot grpmax-eligible | 1.79% | 56 |
| Remaining individualsnot grpmax-eligible | 1.63% | 61 |
| Admixed American | 1.41% | 71 |
| South Asian | 1.18% | 85 |
| Ashkenazi Jewishnot grpmax-eligible | 0.543% | 184 |
| Middle Eastern | 0.384% | 260 |
| African / African-American | 0.353% | 283 |
| Amishnot grpmax-eligible | 0.11% | 912 |
| East Asian | 0.0158% | 6,337 |
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
- ACAA2
- Coding
- c.16+17C>T
- MANE Select
- NM_006111
- Type
- single nucleotide variant
- Location
- chr18:49813452 (GRCh38)
- Gene constraint
- LOEUF 1.148 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.49 · 2 PDB
Similar variants
- ACAA2 p.Tyr198Asn Benign ★★ same type
- ACAA2 p.Ala183Thr Uncertain significance ★ ⚠ same type
- ACAA2 p.Ala196Thr Uncertain significance ★ ⚠ same type
- ACAA2 p.Ala250Thr Uncertain significance ★ ⚠ same type
- ACAA2 p.Ala267Gly Uncertain significance ★ ⚠ same type
- ACAA2 p.Ala70Ser Uncertain significance ★ ⚠ same type
- ACAA2 p.Arg133His Uncertain significance ★ ⚠ same type
- ACAA2 p.Arg371Cys 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/acaa2-c-16-plus-17c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown