BCO1 p.Lys193=
c.579G>A · VCV4931470
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.75%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.25 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.28 | loss · gain 0.07 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 5 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 6.307 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.75%
African / African-American · 1,312/75,042 alleles
Filtering AF
1.67%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.64%
Overall
0.0883%
1,425/1,614,206 alleles · low-frequency
exomes 707/1,461,886 · genomes 718/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.75% | 57 |
| Remaining individualsnot grpmax-eligible | 0.106% | 947 |
| Admixed American | 0.06% | 1,667 |
| South Asian | 0.0022% | 45,540 |
| European (non-Finnish) | 0.000763% | 131,116 |
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.Lys193=
- Coding
- c.579G>A
- MANE Select
- NM_017429
- Type
- single nucleotide variant
- Location
- chr16:81264747 (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-lys193 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown