DCAF15 p.Ile153=
c.459C>T · rs112921664 · VCV782322
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.52%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.55 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.23 | gain · loss 0.13 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -0.12 | GERP -3.1, phastCons 0.53 |
| Overall | ||
| CADD | 17.29 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.52%
African / African-American · 2,638/75,022 alleles
Filtering AF
3.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.36%
Overall
0.188%
3,031/1,613,732 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.52% | 28 |
| Admixed American | 0.218% | 458 |
| Remaining individualsnot grpmax-eligible | 0.203% | 492 |
| Middle Eastern | 0.0825% | 1,212 |
| European (non-Finnish) | 0.0107% | 9,365 |
| South Asian | 0.00439% | 22,767 |
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
- DCAF15
- Protein
- p.Ile153=
- Coding
- c.459C>T
- MANE Select
- NM_138353
- dbSNP
- rs112921664
- Type
- single nucleotide variant
- Location
- chr19:13956004 (GRCh38)
- Gene constraint
- LOEUF 0.502 · pLI 0.97 (gnomAD)
- Structure
- AlphaFold pLDDT 78.92 · 9 PDB
- Residue 153
- a β-strand
Similar variants
- DCAF15 p.Ala149Thr Uncertain significance ★ ⚠ same type
- DCAF15 p.Ala149Val Uncertain significance ★ ⚠ same type
- DCAF15 p.Ala162Gly Uncertain significance ★ ⚠ same type
- DCAF15 p.Ala23Gly Uncertain significance ★ ⚠ same type
- DCAF15 p.Ala2Val Uncertain significance ★ ⚠ same type
- DCAF15 p.Ala303Val Uncertain significance ★ ⚠ same type
- DCAF15 p.Ala305Gly Uncertain significance ★ ⚠ same type
- DCAF15 p.Ala316Thr 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/dcaf15-p-ile153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown