BAZ2B p.Arg1780=
c.5340A>T · VCV3771226
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00667%, 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 2.4 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 8.049 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00667%
Admixed American · 4/59,964 alleles
Filtering AF
0.00226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.000274%
4/1,460,406 alleles · very rare
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.Arg1780=
- Coding
- c.5340A>T
- MANE Select
- NM_013450
- Type
- single nucleotide variant
- Location
- chr2:159347600 (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.Arg1780Gln 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-arg1780 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown