Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.14%, mid)
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 -2.9 | GERP -4.2 |
| Overall | ||
| CADD | 1.387 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.14%
Middle Eastern · 69/6,062 alleles
Filtering AF
0.992%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.986%
Overall
0.861%
13,899/1,614,130 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.14% | 88 |
| European (non-Finnish) | 1.01% | 99 |
| Remaining individualsnot grpmax-eligible | 0.854% | 117 |
| Ashkenazi Jewishnot grpmax-eligible | 0.591% | 169 |
| Admixed American | 0.59% | 170 |
| Amishnot grpmax-eligible | 0.548% | 182 |
| South Asian | 0.448% | 223 |
| African / African-American | 0.428% | 234 |
| Finnishnot grpmax-eligible | 0.225% | 445 |
| East Asian | 0.0111% | 8,977 |
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
- BPI
- Protein
- p.Ser115=
- Coding
- c.345C>T
- MANE Select
- NM_001725
- dbSNP
- rs5743502
- Type
- single nucleotide variant
- Location
- chr20:38309029 (GRCh38)
- Gene constraint
- LOEUF 1.011 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.70 · 2 PDB
- Residue 115
- the 'n-terminal barrel' region; a β-strand
Similar variants
- BPI c.664+7G>T Benign ★★ same type
- BPI p.Ala12Val Benign ★★ same type
- BPI p.Ala192Val Benign ★★ same type
- BPI p.Ala333Thr Likely benign ★★ ⚠ same type
- BPI p.Ala8Thr Benign ★★ same type
- BPI p.Ala8Val Benign ★★ same type
- BPI p.Arg86Cys Benign ★★ ⚠ same type
- BPI p.Glu136Gln Benign ★★ 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/bpi-p-ser115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown