ACSS2 p.Thr628=
c.1884C>T · rs58735881 · VCV3042629
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.107%, nfe)
Conditions
1
ACSS2-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 -11 | GERP -4.5 |
| Overall | ||
| CADD | 0.236 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.107%
European (non-Finnish) · 1,263/1,179,986 alleles
Filtering AF
0.102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.1%
Overall
0.0839%
1,354/1,614,120 alleles · rare
exomes 1,269/1,461,828 · genomes 85/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.107% | 934 |
| Remaining individualsnot grpmax-eligible | 0.0496% | 2,016 |
| African / African-American | 0.0373% | 2,680 |
| Middle Eastern | 0.033% | 3,029 |
| Finnishnot grpmax-eligible | 0.0281% | 3,557 |
| East Asian | 0.0111% | 8,978 |
| Admixed American | 0.005% | 20,007 |
| South Asian | 0.00439% | 22,769 |
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
- ACSS2
- Protein
- p.Thr628=
- Coding
- c.1884C>T
- MANE Select
- NM_018677
- dbSNP
- rs58735881
- Type
- single nucleotide variant
- Location
- chr20:34926262 (GRCh38)
- Gene constraint
- LOEUF 0.785 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.14
Disease context
ACSS2-related disorder
Similar variants
- ACSS2 p.Arg153Gln Uncertain significance ⚠ same condition
- ACSS2 p.Arg696His Uncertain significance same condition
- ACSS2 p.Ala307= Likely benign same condition
- ACSS2 p.Asp309= Likely benign same condition
- ACSS2 p.His252= Benign same condition
- ACSS2 p.Lys342= Likely benign same condition
- ACSS2 p.Pro486= Likely benign same condition
- ACSS2 p.Thr137= Likely benign 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/acss2-p-thr628 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown