This interface displays the predicted impact of gnomAD genetic variants on RNA G-quadruplex (rG4) formation within transcript regions, as evaluated by G4mer.
Each row represents a variant located in the 5′UTR or 3′UTR of a transcript, with G4mer scores computed for both the reference and alternate alleles. The score delta quantifies the change in predicted rG4 probablity due to the variant. We classified the G4 effect of each variant based on how the predicted rG4 confidence changes between the reference and alternate allele. These categories reflect binary classification flips and confidence shifts.
| Effect | Ref Score Range | Alt Score Range | Δ Score Condition | Notes |
|---|---|---|---|---|
| Significantly Breaking | Any > 0.7 | Any < 0.3 | -- | Binary classification flip (strong) |
| Breaking | Any > 0.5 | Any < 0.5 | < -0.2 | Binary classification flip |
| Weakening | Any > 0.7 | -- | < -0.2 | Still G4, but weakened confidence |
| Significantly Forming | All < 0.3 | Any > 0.7 | -- | Binary classification flip (strong) |
| Forming | All < 0.5 | Any > 0.5 | < 0.2 | Binary classification flip |
| Strengthening | All < 0.3 | -- | < 0.2 | Still non-G4, but increased confidence |
You can filter by region and display additional annotations such as ClinVar significance, sequence context, or predicted G4 effect type.
The search bar supports gene/transcript names or IDs (e.g., EPN3) or variant IDs (e.g., rs780750063).
If you have questions or would like additional support, please post on the BioCiphers forum and tag your post with the G4mer label.