TFAP2B p.Asp84=
c.252C>T · rs75279409 · VCV357273
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 4.1%, afr)
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 1.4 | GERP -1.5, phastCons 1 |
| Overall | ||
| CADD | 12.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.1%
African / African-American · 3,077/74,986 alleles
Filtering AF
3.98%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.93%
Overall
0.231%
3,731/1,614,058 alleles · low-frequency
exomes 1,940/1,461,862 · genomes 1,791/152,196 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.1% | 24 |
| Admixed American | 0.34% | 294 |
| Remaining individualsnot grpmax-eligible | 0.328% | 305 |
| Middle Eastern | 0.28% | 357 |
| European (non-Finnish) | 0.0178% | 5,619 |
| South Asian | 0.0165% | 6,072 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0101% | 9,868 |
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.Asp84=
- Coding
- c.252C>T
- MANE Select
- NM_003221
- dbSNP
- rs75279409
- Type
- single nucleotide variant
- Location
- chr6:50823577 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.95 · 1 PDB
- Residue 84
- 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-asp84 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown