BCO1 p.Pro25=
c.75A>T · rs78699050 · VCV3048547
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.41%, 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 -0.78 | GERP -2.4 |
| Overall | ||
| CADD | 1.038 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.41%
African / African-American · 308/75,070 alleles
Filtering AF
0.373%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.358%
Overall
0.0204%
330/1,614,238 alleles · rare
exomes 168/1,461,892 · genomes 162/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.41% | 244 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,209 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.01% | 10,004 |
| European (non-Finnish) | 0.000254% | 393,349 |
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
- BCO1
- Protein
- p.Pro25=
- Coding
- c.75A>T
- MANE Select
- NM_017429
- dbSNP
- rs78699050
- Type
- single nucleotide variant
- Location
- chr16:81245485 (GRCh38)
- Gene constraint
- LOEUF 1.17 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.03
Similar variants
- BCO1 p.Arg266Trp Uncertain significance ★★ ⚠ same type
- BCO1 p.Thr170Met Uncertain significance ★★ ⚠ same type
- BCO1 c.1101+48C>T Benign ★★ same type
- BCO1 c.1102-81T>C Benign ★★ same type
- BCO1 c.1303-13G>A Benign ★★ same type
- BCO1 c.1303-70A>G Benign ★★ same type
- BCO1 c.194-219A>G Benign ★★ same type
- BCO1 c.194-74A>G 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/bco1-p-pro25 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown