Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.35%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.097 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -9.5 | GERP -3.8 |
| Overall | ||
| CADD | 2.938 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.35%
African / African-American · 1,005/74,642 alleles
Filtering AF
1.28%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.25%
Overall
0.0767%
1,231/1,604,748 alleles · low-frequency
exomes 591/1,452,498 · genomes 640/152,250 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.35% | 74 |
| Remaining individualsnot grpmax-eligible | 0.11% | 912 |
| Admixed American | 0.101% | 989 |
| Finnishnot grpmax-eligible | 0.0882% | 1,134 |
| Middle Eastern | 0.083% | 1,204 |
| East Asian | 0.00894% | 11,182 |
| South Asian | 0.00333% | 30,038 |
| European (non-Finnish) | 0.00264% | 37,920 |
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
- CTDSP1
- Protein
- p.Ser58=
- Coding
- c.174C>T
- MANE Select
- NM_021198
- dbSNP
- rs2227250
- Type
- single nucleotide variant
- Location
- chr2:218401670 (GRCh38)
- Gene constraint
- LOEUF 0.686 · pLI 0.09 (gnomAD)
- Structure
- AlphaFold pLDDT 82.13 · 11 PDB
Similar variants
- CTDSP1 p.Ser58Asn Uncertain significance ★ ⚠ same residue
- CTDSP1 p.Ala56Thr Benign ★★ same type
- CTDSP1 p.Ala15Thr Uncertain significance ★ ⚠ same type
- CTDSP1 p.Ala15Val Uncertain significance ★ ⚠ same type
- CTDSP1 p.Ala163Val Uncertain significance ★ ⚠ same type
- CTDSP1 p.Ala171Val Uncertain significance ★ ⚠ same type
- CTDSP1 p.Ala174Ser Uncertain significance ★ ⚠ same type
- CTDSP1 p.Ala56Val 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/ctdsp1-p-ser58 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown