BCOR c.165+166C>T
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.25%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +166 | deep intronic (+166 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.52 | GERP -0.86 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 8.941 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.25%
African / African-American · 1,309/30,771 alleles
Filtering AF
4.06%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.99%
Overall
1.22%
1,368/112,003 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.25% | 24 |
| Remaining individualsnot grpmax-eligible | 1.17% | 86 |
| Admixed American | 0.311% | 321 |
| European (non-Finnish) | 0.015% | 6,647 |
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
- BCOR
- Coding
- c.165+166C>T
- MANE Select
- NM_001123385
- dbSNP
- rs140614926
- Type
- single nucleotide variant
- Location
- chrX:40076288 (GRCh38)
- Structure
- AlphaFold pLDDT 39.82 · 5 PDB
Similar variants
- BCOR p.Arg1163Ter Pathogenic ★★ same type
- BCOR p.Arg1164Ter Pathogenic ★★ same type
- BCOR p.Arg1217Ter Pathogenic ★★ same type
- BCOR p.Arg1514Ter Pathogenic ★★ same type
- BCOR p.Arg342Ter Pathogenic ★★ same type
- BCOR p.Arg810Ter Pathogenic ★★ same type
- BCOR p.Arg976Ter Pathogenic ★★ same type
- BCOR p.Ala1262Ser 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/bcor-c-165-plus-166c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown