ARL3 c.147+17C>T
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0953%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +17 | near-intronic (+17 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.95 | GERP 1.6 |
| Non-coding constraint | Z 0.66 | 1 kb window · o/e 0.95 · regional · uncalibrated |
| Overall | ||
| CADD | 12.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0953%
African / African-American · 70/73,472 alleles
Filtering AF
0.0773%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0707%
Overall
0.0048%
74/1,542,960 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0953% | 1,050 |
| Admixed American | 0.00366% | 27,346 |
| Remaining individualsnot grpmax-eligible | 0.0017% | 58,836 |
| European (non-Finnish) | 8.82e-05% | 1,134,131 |
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
- ARL3
- Coding
- c.147+17C>T
- MANE Select
- NM_004311
- dbSNP
- rs192947915
- Type
- single nucleotide variant
- Location
- chr10:102705329 (GRCh38)
- Gene constraint
- LOEUF 0.557 · pLI 0.93 (gnomAD)
- Structure
- AlphaFold pLDDT 92.73
Similar variants
- ARL3 p.Gly70Glu Pathogenic/Likely pathogenic ★★ same type
- ARL3 c.3+1G>A Uncertain significance ★★ same type
- ARL3 c.3+2T>C Uncertain significance ★★ same type
- ARL3 c.3+3G>T Uncertain significance ★★ same type
- ARL3 c.316-2A>G Uncertain significance ★★ same type
- ARL3 p.Ala13Ser Uncertain significance ★★ ⚠ same type
- ARL3 p.Ala140Val Uncertain significance ★★ ⚠ same type
- ARL3 p.Ala179Pro 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/arl3-c-147-plus-17c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown