DBF4 p.Ile18=
c.54C>A · rs34483317 · VCV792081
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.29%, afr)
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 -0.036 | GERP -1.9, phastCons 0.72 |
| Overall | ||
| CADD | 7.696 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.29%
African / African-American · 3,175/73,930 alleles
Filtering AF
4.17%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.12%
Overall
0.221%
3,535/1,596,988 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.29% | 23 |
| Admixed American | 0.266% | 376 |
| Remaining individualsnot grpmax-eligible | 0.264% | 378 |
| Middle Eastern | 0.159% | 628 |
| South Asian | 0.0126% | 7,947 |
| European (non-Finnish) | 0.0023% | 43,489 |
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
- DBF4
- Protein
- p.Ile18=
- Coding
- c.54C>A
- MANE Select
- NM_006716
- dbSNP
- rs34483317
- Type
- single nucleotide variant
- Location
- chr7:87878060 (GRCh38)
- Gene constraint
- LOEUF 0.475 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 55.17 · 7 PDB
- Residue 18
- the 'disordered' region
Similar variants
- DBF4 p.Lys579Glu Benign ★★ same type
- DBF4 p.Ala661Val Uncertain significance ★ ⚠ same type
- DBF4 p.Arg101Gln Uncertain significance ★ ⚠ same type
- DBF4 p.Arg214Lys Uncertain significance ★ ⚠ same type
- DBF4 p.Arg26Gly Uncertain significance ★ ⚠ same type
- DBF4 p.Arg576Gln Uncertain significance ★ ⚠ same type
- DBF4 p.Arg599Gly Uncertain significance ★ ⚠ same type
- DBF4 p.Asn317Ser 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/dbf4-p-ile18 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown