BAZ1B p.Ser1293=
c.3879C>T · VCV4084656
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00169%, amr)
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 -2.3 | GERP -3.7 |
| Overall | ||
| CADD | 1.945 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00169%
Admixed American · 1/59,024 alleles
Filtering AF
0.000247%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000159%
Overall
0.000621%
10/1,610,398 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00169% | 59,024 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,366 |
| South Asian | 0.00111% | 90,462 |
| European (non-Finnish) | 0.000594% | 168,377 |
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
- BAZ1B
- Protein
- p.Ser1293=
- Coding
- c.3879C>T
- MANE Select
- NM_032408
- Type
- single nucleotide variant
- Location
- chr7:73444095 (GRCh38)
- Gene constraint
- LOEUF 0.201 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.55 · 2 PDB
- Residue 1293
- the 'disordered' region
Similar variants
- BAZ1B p.Glu720Asp Uncertain significance ★★ ⚠ same type
- BAZ1B c.3581-6C>T Likely benign ★★ same type
- BAZ1B p.Arg1340Lys Likely benign ★★ same type
- BAZ1B p.Gln1434= Benign ★★ same type
- BAZ1B p.Glu1142= Benign/Likely benign ★★ same type
- BAZ1B p.His939Tyr Benign ★★ same type
- BAZ1B p.Pro1448= Benign/Likely benign ★★ same type
- BAZ1B p.Ser679= 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/baz1b-p-ser1293 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown