AR c.1616+3A>C
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +3 | donor splice region (+3, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Pangolin | Δ0.66 | loss · gain 0.01 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 6.8 | GERP 2.1, phastCons 1 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 22.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- AR
- Coding
- c.1616+3A>C
- MANE Select
- NM_000044
- dbSNP
- rs1057518601
- Type
- single nucleotide variant
- Location
- chrX:67546765 (GRCh38)
- Structure
- AlphaFold pLDDT 58.85 · 95 PDB
Similar variants
- AR c.1768+2T>C Pathogenic/Likely pathogenic ★★ same type
- AR c.1769-11T>A Pathogenic ★★ same type
- AR c.2450-6C>G Pathogenic ★★ same type
- AR p.Ala588Pro Pathogenic/Likely pathogenic ★★ same type
- AR p.Ala597Thr Pathogenic ★★ same type
- AR p.Ala688Val Pathogenic/Likely pathogenic ★★ same type
- AR p.Ala766Thr Pathogenic ★★ same type
- AR p.Ala871Val Pathogenic/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/ar-c-1616-plus-3a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown