ARF1 p.Val100=
c.300G>A · rs147354087 · VCV3040638
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.817%, afr)
Conditions
1
ARF1-related disorder
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 0.66 | GERP -1.9, phastCons 1 |
| Overall | ||
| CADD | 5.414 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.817%
African / African-American · 613/75,040 alleles
Filtering AF
0.763%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.742%
Overall
0.0423%
682/1,614,166 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.817% | 122 |
| Remaining individualsnot grpmax-eligible | 0.0576% | 1,736 |
| Middle Eastern | 0.0495% | 2,021 |
| Admixed American | 0.0417% | 2,401 |
| South Asian | 0.0022% | 45,544 |
| European (non-Finnish) | 0.000254% | 393,338 |
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
- ARF1
- Protein
- p.Val100=
- Coding
- c.300G>A
- MANE Select
- NM_001658
- dbSNP
- rs147354087
- Type
- single nucleotide variant
- Location
- chr1:228097631 (GRCh38)
- Gene constraint
- LOEUF 0.247 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.93 · 40 PDB
- Residue 100
- an α-helix
Disease context
ARF1-related disorder
Similar variants
- ARF1 p.Tyr35Asp Pathogenic/Likely pathogenic ★★ same condition
- ARF1 p.Leu148= Likely benign same condition
- ARF1 p.Thr55= Likely benign same condition
- ARF1 p.Arg19Cys Likely pathogenic ★★ same type
- ARF1 p.Arg99His Pathogenic/Likely pathogenic ★★ same type
- ARF1 p.Gly70Ser Likely pathogenic ★★ same type
- ARF1 p.Thr48Ile Likely pathogenic ★★ same type
- ARF1 p.Arg99Cys 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/arf1-p-val100 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown