ARF3 p.His80=
c.240C>T · rs2228417 · VCV1304691
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 19%, sas) — too common for a highly-penetrant pathogenic allele
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 3.8 | GERP 0.058, phastCons 1 |
| Overall | ||
| CADD | 8.167 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
19%
South Asian · 17,310/91,054 alleles
Filtering AF
18.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 18.7%
Overall
7.11%
114,694/1,613,860 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 19% | 5 |
| Middle Eastern | 11.6% | 9 |
| Ashkenazi Jewishnot grpmax-eligible | 7.85% | 13 |
| Remaining individualsnot grpmax-eligible | 7.54% | 13 |
| European (non-Finnish) | 7% | 14 |
| Finnishnot grpmax-eligible | 5.17% | 19 |
| Admixed American | 4.1% | 24 |
| Amishnot grpmax-eligible | 2.74% | 36 |
| African / African-American | 1.33% | 75 |
| East Asian | 0.524% | 191 |
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
- ARF3
- Protein
- p.His80=
- Coding
- c.240C>T
- MANE Select
- NM_001659
- dbSNP
- rs2228417
- Type
- single nucleotide variant
- Location
- chr12:48940016 (GRCh38)
- Gene constraint
- LOEUF 0.485 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 86.23 · 2 PDB
- Residue 80
- an α-helix
Similar variants
- ARF3 p.Asp93Asn Pathogenic/Likely pathogenic ★★ same type
- ARF3 p.Arg19Cys Pathogenic ★ same type
- ARF3 p.Arg99Leu Likely pathogenic ★ same type
- ARF3 p.Asn126Asp Likely pathogenic ★ same type
- ARF3 p.Asn60Ile Likely pathogenic ★ same type
- ARF3 p.Asp67Ala Likely pathogenic ★ same type
- ARF3 p.Asp67Val Pathogenic ★ same type
- ARF3 p.Leu12Val 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/arf3-p-his80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown