BUB1 c.567+7del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +7 | near-intronic (+7 nt from the splice site) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.14 | |
| Non-coding constraint | Z 0.31 | 1 kb window · o/e 0.98 · regional · uncalibrated |
| Overall | ||
| CADD | 0.183 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
Admixed American · 4/59,922 alleles
Filtering AF
0.00226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.000575%
9/1,565,508 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00668% | 14,981 |
| European (non-Finnish) | 0.00044% | 227,168 |
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
- BUB1
- Coding
- c.567+7del
- MANE Select
- NM_004336
- Type
- Deletion
- Location
- chr2:110669446 (GRCh38)
- Gene constraint
- LOEUF 0.727 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.91 · 11 PDB
Similar variants
- BUB1 p.Gln170fs Uncertain significance ★ same type
- BUB1 p.Gln503fs Uncertain significance ★ same type
- BUB1 p.Lys1053fs Uncertain significance ★ same type
- BUB1 c.1699-20del Likely benign ★ same type
- BUB1 c.958-15del Likely benign ★ same type
- BUB1 p.His1024fs Pathogenic 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/bub1-c-567-plus-7del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown