BRD4 p.Val1110del
c.3322GTG[2] · rs771140069 · VCV2415289
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.134%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 17.46 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.134%
East Asian · 60/44,836 alleles
Filtering AF
0.107%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0969%
Overall
0.00614%
99/1,612,050 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.134% | 747 |
| South Asian | 0.011% | 9,106 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,821 |
| European (non-Finnish) | 0.00212% | 47,190 |
| Finnishnot grpmax-eligible | 0.0016% | 62,422 |
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
- BRD4
- Protein
- p.Val1110del
- Coding
- c.3322GTG[2]
- MANE Select
- NM_001379291
- dbSNP
- rs771140069
- Type
- Microsatellite
- Location
- chr19:15239774 (GRCh38)
- Gene constraint
- LOEUF 0.191 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 56.20 · 613 PDB
- Residue 1110
- the 'c-terminal (ctd) region' region; a UniProt-annotated variant site (found in a patient with a neurodevelopmental syndrome; likely pathogenic)
Similar variants
- BRD4 p.Val1110Leu Likely benign ★ ⚠ same residue
- BRD4 p.Glu506del Uncertain significance ★★ same type
- BRD4 c.2212-28GTCT[3] Likely benign ★★ same type
- BRD4 p.Glu1113del Benign ★★ same type
- BRD4 p.981QP[1] Uncertain significance ★ same type
- BRD4 p.Gln1289_Arg1290insGln Uncertain significance ★ same type
- BRD4 p.Gln1289del Uncertain significance ★ same type
- BRD4 p.Gln1300_Ala1301insGlnGln 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/brd4-p-val1110del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown