DNAAF4 p.Phe34=
c.102C>T · rs377201923 · VCV454956
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0217%, 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 2.1 | GERP -1.8, phastCons 1 |
| Overall | ||
| CADD | 11.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0217%
Admixed American · 13/59,982 alleles
Filtering AF
0.0127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0101%
Overall
0.00843%
136/1,613,860 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0217% | 4,614 |
| European (non-Finnish) | 0.0103% | 9,752 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,466 |
| African / African-American | 0.00133% | 74,928 |
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
- DNAAF4
- Protein
- p.Phe34=
- Coding
- c.102C>T
- MANE Select
- NM_130810
- dbSNP
- rs377201923
- Type
- single nucleotide variant
- Location
- chr15:55498228 (GRCh38)
- Gene constraint
- LOEUF 1.018 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.00
- Residue 34
- the cs domain; the 'mediates interaction with esr1 and stub1' region
Similar variants
- DNAAF4 p.Phe34Val Uncertain significance ★ ⚠ same residue
- DNAAF4 c.1047+1G>A Pathogenic/Likely pathogenic ★★ same type
- DNAAF4 c.1153+1G>A Pathogenic ★★ same type
- DNAAF4 c.405+1G>A Likely pathogenic ★★ same type
- DNAAF4 p.Arg245Ter Pathogenic/Likely pathogenic ★★ same type
- DNAAF4 p.Arg270Ter Pathogenic/Likely pathogenic ★★ same type
- DNAAF4 p.Arg330Trp Pathogenic/Likely pathogenic ★★ same type
- DNAAF4 p.Arg371Ter Pathogenic/Likely pathogenic ★★ 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/dnaaf4-p-phe34 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown