BPIFB1 p.Pro4=
c.12G>A · rs34388907 · VCV786969
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.693%, 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 -6.8 | GERP -3.5 |
| Overall | ||
| CADD | 0.562 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.693%
African / African-American · 520/75,052 alleles
Filtering AF
0.644%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.624%
Overall
0.044%
711/1,614,126 alleles · rare
exomes 402/1,461,854 · genomes 309/152,272 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.693% | 144 |
| Admixed American | 0.0683% | 1,464 |
| Remaining individualsnot grpmax-eligible | 0.0672% | 1,488 |
| Middle Eastern | 0.0495% | 2,019 |
| European (non-Finnish) | 0.00839% | 11,919 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00675% | 14,804 |
| South Asian | 0.00439% | 22,769 |
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
- BPIFB1
- Protein
- p.Pro4=
- Coding
- c.12G>A
- MANE Select
- NM_033197
- dbSNP
- rs34388907
- Type
- single nucleotide variant
- Location
- chr20:33286085 (GRCh38)
- Gene constraint
- LOEUF 0.795 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.26
Similar variants
- BPIFB1 p.Lys39Arg Benign ★★ same type
- BPIFB1 p.Pro113Ser Benign ★★ same type
- BPIFB1 p.Thr140Ala Benign ★★ same type
- BPIFB1 p.Ala314Ser Uncertain significance ★ ⚠ same type
- BPIFB1 p.Ala328Pro Uncertain significance ★ ⚠ same type
- BPIFB1 p.Ala467Thr Uncertain significance ★ ⚠ same type
- BPIFB1 p.Ala49Ser Uncertain significance ★ ⚠ same type
- BPIFB1 p.Ala49Thr 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/bpifb1-p-pro4 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown