BAZ2B p.Val1803=
c.5409A>T · VCV4083722
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.106%, nfe)
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 -0.17 | GERP 0.6, phastCons 0.7 |
| Overall | ||
| CADD | 5.103 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.106%
European (non-Finnish) · 1,245/1,179,850 alleles
Filtering AF
0.101%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0987%
Overall
0.0812%
1,310/1,613,884 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.106% | 948 |
| Remaining individualsnot grpmax-eligible | 0.0608% | 1,645 |
| Middle Eastern | 0.0495% | 2,019 |
| Admixed American | 0.015% | 6,669 |
| African / African-American | 0.0107% | 9,381 |
| Finnishnot grpmax-eligible | 0.00781% | 12,800 |
| South Asian | 0.0022% | 45,538 |
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.Val1803=
- Coding
- c.5409A>T
- MANE Select
- NM_013450
- Type
- single nucleotide variant
- Location
- chr2:159347531 (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.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
- BAZ2B p.Pro1709Ser 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-val1803 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown