ARF6 p.Leu17=
c.51C>T · rs114513764 · VCV710032
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.98%, 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 4.2 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 13.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.98%
African / African-American · 1,485/75,064 alleles
Filtering AF
1.89%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.86%
Overall
0.101%
1,637/1,614,232 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.98% | 51 |
| Admixed American | 0.112% | 896 |
| Remaining individualsnot grpmax-eligible | 0.0976% | 1,025 |
| Middle Eastern | 0.0825% | 1,212 |
| South Asian | 0.00878% | 11,385 |
| East Asian | 0.00223% | 44,890 |
| European (non-Finnish) | 0.000847% | 118,004 |
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
- ARF6
- Protein
- p.Leu17=
- Coding
- c.51C>T
- MANE Select
- NM_001663
- dbSNP
- rs114513764
- Type
- single nucleotide variant
- Location
- chr14:49893787 (GRCh38)
- Gene constraint
- LOEUF 0.251 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 94.24 · 20 PDB
- Residue 17
- a β-strand
Similar variants
- ARF6 p.Leu73= Benign ★★ same type
- ARF6 p.Asp63Asn Uncertain significance ★ ⚠ same type
- ARF6 p.Met130Val Uncertain significance ★ ⚠ same type
- ARF6 p.Ser158Thr Uncertain significance ★ ⚠ same type
- ARF6 p.Thr170Ile Uncertain significance ★ same type
- ARF6 p.Tyr163Cys 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/arf6-p-leu17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown