BCO2 p.Pro244=
c.732A>C · rs149790013 · VCV2642372
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.379%, sas)
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 0.85 | GERP 0.72 |
| Overall | ||
| CADD | 3.023 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.379%
South Asian · 338/89,240 alleles
Filtering AF
0.346%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.332%
Overall
0.271%
4,297/1,587,752 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.379% | 264 |
| European (non-Finnish) | 0.299% | 335 |
| Finnishnot grpmax-eligible | 0.283% | 354 |
| Remaining individualsnot grpmax-eligible | 0.269% | 372 |
| Ashkenazi Jewishnot grpmax-eligible | 0.153% | 653 |
| Admixed American | 0.115% | 871 |
| Middle Eastern | 0.0998% | 1,002 |
| African / African-American | 0.0324% | 3,089 |
| East Asian | 0.00897% | 11,153 |
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
- BCO2
- Protein
- p.Pro244=
- Coding
- c.732A>C
- MANE Select
- NM_031938
- dbSNP
- rs149790013
- Type
- single nucleotide variant
- Location
- chr11:112194751 (GRCh38)
- Gene constraint
- LOEUF 1.047 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.41
Similar variants
- BCO2 p.Arg472Ter Likely benign ★★ same type
- BCO2 p.Ala115Val Uncertain significance ★ ⚠ same type
- BCO2 p.Ala223Gly Uncertain significance ★ ⚠ same type
- BCO2 p.Ala318Val Uncertain significance ★ ⚠ same type
- BCO2 p.Ala437Ser Uncertain significance ★ ⚠ same type
- BCO2 p.Arg184Trp Uncertain significance ★ ⚠ same type
- BCO2 p.Arg253Gln Uncertain significance ★ ⚠ same type
- BCO2 p.Arg27Trp 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/bco2-p-pro244 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown