GFI1 p.Phe293=
c.879C>T · VCV4827134
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00196%, 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 -0.016 | GERP -0.31, phastCons 0.31 |
| Overall | ||
| CADD | 9.274 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00196%
Admixed American · 1/50,978 alleles
Overall
0.000194%
3/1,550,236 alleles · very rare
exomes 2/1,398,048 · genomes 1/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00196% | 50,978 |
| African / African-American | 0.00137% | 73,032 |
| European (non-Finnish) | 8.72e-05% | 1,146,682 |
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
- GFI1
- Protein
- p.Phe293=
- Coding
- c.879C>T
- MANE Select
- NM_005263
- Type
- single nucleotide variant
- Location
- chr1:92480393 (GRCh38)
- Gene constraint
- LOEUF 0.715 · pLI 0.05 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.33
Similar variants
- GFI1 p.Asn382Ser Pathogenic ★★ ⚠ same type
- GFI1 p.Ala128Glu Uncertain significance ★★ ⚠ same type
- GFI1 p.Ala128Gly Uncertain significance ★★ ⚠ same type
- GFI1 p.Ala144Gly Uncertain significance ★★ ⚠ same type
- GFI1 p.Ala158Ser Uncertain significance ★★ ⚠ same type
- GFI1 p.Ala165Asp Uncertain significance ★★ ⚠ same type
- GFI1 p.Ala174Val Uncertain significance ★★ ⚠ same type
- GFI1 p.Ala179Thr 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/gfi1-p-phe293 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown