VGF p.Arg308=
c.922C>A · rs200560795 · VCV722382
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.728%, 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 0.81 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 8.278 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.728%
African / African-American · 492/67,622 alleles
Filtering AF
0.674%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.653%
Overall
0.0371%
541/1,460,090 alleles · rare
exomes 229/1,307,816 · genomes 312/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.728% | 137 |
| Admixed American | 0.0584% | 1,712 |
| Remaining individualsnot grpmax-eligible | 0.0408% | 2,452 |
| Middle Eastern | 0.0238% | 4,200 |
| South Asian | 0.00138% | 72,388 |
| European (non-Finnish) | 0.000179% | 558,903 |
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
- VGF
- Protein
- p.Arg308=
- Coding
- c.922C>A
- MANE Select
- NM_003378
- dbSNP
- rs200560795
- Type
- single nucleotide variant
- Location
- chr7:101163922 (GRCh38)
- Gene constraint
- LOEUF 0.864 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.87 · 7 PDB
Similar variants
- VGF p.Glu107Gln Benign ★★ same type
- VGF p.Leu327= Benign ★★ same type
- VGF p.Pro492= Benign/Likely benign ★★ same type
- VGF p.Ala149Val Uncertain significance ★ ⚠ same type
- VGF p.Ala160Glu Uncertain significance ★ ⚠ same type
- VGF p.Ala181Glu Uncertain significance ★ ⚠ same type
- VGF p.Ala233Glu Uncertain significance ★ ⚠ same type
- VGF p.Ala30Val 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/vgf-p-arg308 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown