BBOX1 p.Ala207=
c.621C>T · rs76937267 · VCV780965
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.07%, afr)
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 -1.1 | GERP -1.8, phastCons 0.001 |
| Overall | ||
| CADD | 5.557 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.07%
African / African-American · 3,036/74,634 alleles
Filtering AF
3.95%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.9%
Overall
0.257%
4,145/1,609,888 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.07% | 25 |
| Middle Eastern | 0.431% | 232 |
| Admixed American | 0.352% | 284 |
| Remaining individualsnot grpmax-eligible | 0.327% | 305 |
| Ashkenazi Jewishnot grpmax-eligible | 0.214% | 468 |
| European (non-Finnish) | 0.0498% | 2,006 |
| South Asian | 0.0187% | 5,340 |
| Finnishnot grpmax-eligible | 0.00313% | 31,962 |
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
- BBOX1
- Protein
- p.Ala207=
- Coding
- c.621C>T
- MANE Select
- NM_003986
- dbSNP
- rs76937267
- Type
- single nucleotide variant
- Location
- chr11:27115539 (GRCh38)
- Gene constraint
- LOEUF 0.983 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.06 · 12 PDB
Similar variants
- BBOX1 p.Phe310= Benign ★★ same type
- BBOX1 p.Tyr133= Benign ★★ same type
- BBOX1 p.Ala14Asp Uncertain significance ★ ⚠ same type
- BBOX1 p.Ala155Thr Uncertain significance ★ ⚠ same type
- BBOX1 p.Ala193Ser Uncertain significance ★ ⚠ same type
- BBOX1 p.Ala248Val Uncertain significance ★ ⚠ same type
- BBOX1 p.Ala354Thr Uncertain significance ★ ⚠ same type
- BBOX1 p.Arg288Cys 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/bbox1-p-ala207 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown