ACP1 p.Thr32=
c.96C>T · rs142497773 · VCV756151
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 -1.4 | GERP -3.7 |
| Overall | ||
| CADD | 7.229 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,082 alleles
Filtering AF
0.00626%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00469%
Overall
0.00285%
46/1,612,950 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,082 |
| African / African-American | 0.0121% | 8,292 |
| Finnishnot grpmax-eligible | 0.00313% | 31,912 |
| European (non-Finnish) | 0.00254% | 39,321 |
| East Asian | 0.00223% | 44,842 |
| South Asian | 0.0022% | 45,526 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,464 |
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
- ACP1
- Protein
- p.Thr32=
- Coding
- c.96C>T
- MANE Select
- NM_004300
- dbSNP
- rs142497773
- Type
- single nucleotide variant
- Location
- chr2:271918 (GRCh38)
- Gene constraint
- LOEUF 1.547 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.16 · 17 PDB
- Residue 32
- an α-helix
Similar variants
- ACP1 c.43+10C>T Benign ★★ same type
- ACP1 c.43+8G>A Benign ★★ same type
- ACP1 p.Gly134= Benign ★★ same type
- ACP1 p.Lys7Asn Benign ★★ ⚠ same type
- ACP1 p.Thr141= Benign ★★ same type
- ACP1 c.231+100G>T Uncertain significance ★ same type
- ACP1 c.231+49T>C Uncertain significance ★ same type
- ACP1 c.231+57G>A 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/acp1-p-thr32 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown