BAZ2B p.Pro821=
c.2463G>A · VCV4084862
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.413 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.58 | GERP -3.7, phastCons 0.019 |
| Overall | ||
| CADD | 11.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,054 alleles
Filtering AF
0.00318%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00287%
Overall
0.00354%
57/1,612,272 alleles · ultra-rare
exomes 57/1,460,112 · genomes 0/152,160 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,054 |
| East Asian | 0.00446% | 22,398 |
| European (non-Finnish) | 0.00416% | 24,053 |
| South Asian | 0.0033% | 30,331 |
| Admixed American | 0.00167% | 59,960 |
| African / African-American | 0.00133% | 74,960 |
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
- BAZ2B
- Protein
- p.Pro821=
- Coding
- c.2463G>A
- MANE Select
- NM_013450
- Type
- single nucleotide variant
- Location
- chr2:159427944 (GRCh38)
- Gene constraint
- LOEUF 0.386 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 55.23 · 265 PDB
Similar variants
- BAZ2B p.Pro821Leu Uncertain significance ★ ⚠ same residue
- BAZ2B p.Met1Thr Pathogenic/Likely pathogenic ★★ same type
- BAZ2B p.Arg1290Gln Uncertain significance ★★ ⚠ same type
- BAZ2B p.Ile502Val Uncertain significance ★★ ⚠ same type
- BAZ2B p.Leu1365Pro Uncertain significance ★★ ⚠ same type
- BAZ2B p.Leu587Ser Uncertain significance ★★ ⚠ same type
- BAZ2B p.Lys1761Asn Uncertain significance ★★ ⚠ same type
- BAZ2B p.Met1013Ile 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/baz2b-p-pro821 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown