CSTA c.*10C>T
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Conditions
1
CSTA-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 -0.59 | GERP -2 |
| Non-coding constraint | Z 0.86 | 1 kb window · o/e 0.93 · regional · uncalibrated |
| Overall | ||
| CADD | 1.367 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,888 alleles
Filtering AF
0.0005%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000366%
Overall
0.000805%
13/1,613,940 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,888 |
| Admixed American | 0.00167% | 59,984 |
| European (non-Finnish) | 0.000932% | 107,273 |
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
- CSTA
- Coding
- c.*10C>T
- MANE Select
- NM_005213
- dbSNP
- rs1382133964
- Type
- single nucleotide variant
- Location
- chr3:122341577 (GRCh38)
- Gene constraint
- LOEUF 1.219 · pLI 0.12 (gnomAD)
- Structure
- AlphaFold pLDDT 93.57 · 14 PDB
Disease context
CSTA-related disorder
Similar variants
- CSTA p.Arg58Ter Likely pathogenic ★★ same type
- CSTA p.Lys22Ter Pathogenic ★★ same type
- CSTA c.169-12A>C Benign ★★ same type
- CSTA p.Lys91Asn Benign ★★ ⚠ same type
- CSTA p.Thr96Met Benign ★★ ⚠ same type
- CSTA p.Tyr35= Benign ★★ same type
- CSTA c.67-2A>T Pathogenic ★ same type
- CSTA p.Tyr35Ter Likely pathogenic ★ 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/csta-c-star-10c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown