TAF4 p.Ala3=
c.9G>A · VCV4821107
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.203%, 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 6 | GERP 0.35, phastCons 1 |
| Overall | ||
| CADD | 17.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.203%
African / African-American · 128/62,942 alleles
Filtering AF
0.175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.164%
Overall
0.0115%
150/1,303,584 alleles · rare
exomes 59/1,156,882 · genomes 91/146,702 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.203% | 492 |
| Finnishnot grpmax-eligible | 0.0377% | 2,655 |
| Remaining individualsnot grpmax-eligible | 0.0134% | 7,480 |
| Admixed American | 0.0078% | 12,823 |
| European (non-Finnish) | 0.000199% | 502,540 |
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
- TAF4
- Protein
- p.Ala3=
- Coding
- c.9G>A
- MANE Select
- NM_003185
- Type
- single nucleotide variant
- Location
- chr20:62065802 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.71 · 32 PDB
Similar variants
- TAF4 p.Ala153Val Uncertain significance ★★ ⚠ same type
- TAF4 p.Ala251Thr Uncertain significance ★★ ⚠ same type
- TAF4 p.Arg774Gln Uncertain significance ★★ ⚠ same type
- TAF4 p.Gly171Cys Uncertain significance ★★ ⚠ same type
- TAF4 p.Gly306Glu Uncertain significance ★★ ⚠ same type
- TAF4 p.Leu58Val Uncertain significance ★★ ⚠ same type
- TAF4 p.Pro241Leu Uncertain significance ★★ ⚠ same type
- TAF4 p.Asn220Ser Likely benign ★★ 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/taf4-p-ala3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown