BCO1 p.Ala165=
c.495G>A · rs369214485 · VCV3030112
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00533%, afr)
Conditions
1
BCO1-related disorder
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 -2.1 | GERP -4 |
| Overall | ||
| CADD | 5.664 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00533%
African / African-American · 4/75,004 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00123%
Overall
0.00198%
32/1,614,072 alleles · very rare
exomes 29/1,461,838 · genomes 3/152,234 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00533% | 18,751 |
| South Asian | 0.0022% | 45,539 |
| European (non-Finnish) | 0.00212% | 47,199 |
| Admixed American | 0.00167% | 60,018 |
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.Ala165=
- Coding
- c.495G>A
- MANE Select
- NM_017429
- dbSNP
- rs369214485
- Type
- single nucleotide variant
- Location
- chr16:81264663 (GRCh38)
- Gene constraint
- LOEUF 1.17 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.03
Disease context
BCO1-related disorder
Similar variants
- BCO1 c.1102-10A>G Likely benign same condition
- BCO1 p.Asp52= Likely benign same condition
- BCO1 p.Ile324Thr Likely benign ⚠ same condition
- 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
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-ala165 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown