ACSS2 p.Asp309=
c.927C>T · rs370544852 · VCV3055005
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00585%, 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 2.8 | GERP -0.75, phastCons 1 |
| Overall | ||
| CADD | 10.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00585%
European (non-Finnish) · 69/1,179,952 alleles
Filtering AF
0.0047%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00431%
Overall
0.00465%
75/1,611,704 alleles · very rare
exomes 65/1,460,060 · genomes 10/151,644 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00585% | 17,101 |
| Admixed American | 0.00334% | 29,973 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,166 |
| Finnishnot grpmax-eligible | 0.00157% | 63,772 |
| African / African-American | 0.00134% | 74,622 |
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.Asp309=
- Coding
- c.927C>T
- MANE Select
- NM_018677
- dbSNP
- rs370544852
- Type
- single nucleotide variant
- Location
- chr20:34919527 (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.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
- ACSS2 p.Thr628= 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-asp309 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown