TFAP2B p.His30=
c.90C>T · rs959819079 · VCV1902961
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0023%, eas)
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 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 12.11 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0023%
East Asian · 1/43,490 alleles
Overall
0.000188%
3/1,594,002 alleles · very rare
exomes 2/1,442,078 · genomes 1/151,924 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0023% | 43,490 |
| Admixed American | 0.00175% | 57,244 |
| European (non-Finnish) | 8.54e-05% | 1,170,634 |
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
- TFAP2B
- Protein
- p.His30=
- Coding
- c.90C>T
- MANE Select
- NM_003221
- dbSNP
- rs959819079
- Type
- single nucleotide variant
- Location
- chr6:50823415 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.95 · 1 PDB
- Residue 30
- the 'disordered' region
Similar variants
- TFAP2B p.Arg236His Likely pathogenic ★★ same type
- TFAP2B p.Arg285Gln Pathogenic/Likely pathogenic ★★ same type
- TFAP2B p.Ala54Gly Uncertain significance ★★ same type
- TFAP2B p.Asp31Gly Uncertain significance ★★ ⚠ same type
- TFAP2B p.Asp346Glu Uncertain significance ★★ same type
- TFAP2B p.Pro205Ser Uncertain significance ★★ ⚠ same type
- TFAP2B p.Ser277Trp Uncertain significance ★★ ⚠ same type
- TFAP2B p.Thr306Met 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/tfap2b-p-his30 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown