BRPF1 p.Val99=
c.297G>A · rs147247799 · VCV799387
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.117%, 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 0.73 | GERP -1.9, phastCons 1 |
| Overall | ||
| CADD | 7.349 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.117%
African / African-American · 88/75,024 alleles
Filtering AF
0.0975%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0901%
Overall
0.00638%
103/1,614,136 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.117% | 853 |
| Admixed American | 0.01% | 10,003 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,419 |
| South Asian | 0.0011% | 91,076 |
| European (non-Finnish) | 0.000169% | 590,012 |
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
- BRPF1
- Protein
- p.Val99=
- Coding
- c.297G>A
- MANE Select
- NM_001003694
- dbSNP
- rs147247799
- Type
- single nucleotide variant
- Location
- chr3:9734437 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.74 · 66 PDB
- Residue 99
- a UniProt-annotated variant site (in idddfp); the 'interaction with kat6a and kat6b' region
Similar variants
- BRPF1 p.Arg1100Ter Pathogenic/Likely pathogenic ★★ same type
- BRPF1 p.Arg251Ter Pathogenic ★★ same type
- BRPF1 p.Arg455Ter Pathogenic ★★ same type
- BRPF1 p.Trp478Ter Pathogenic/Likely pathogenic ★★ same type
- BRPF1 p.Ala363Thr Uncertain significance ★★ ⚠ same type
- BRPF1 p.Ala601Thr Uncertain significance ★★ ⚠ same type
- BRPF1 p.Arg106Cys Uncertain significance ★★ ⚠ same type
- BRPF1 p.Arg157His 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/brpf1-p-val99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown