Frequently Asked Questions
General Information
What is NC-Scorer?
NC-Scorer (Nephro Candidate Scorer) is a web-based application designed to help researchers evaluate genetic variants for their potential involvement in kidney disease. It uses a specialized scoring algorithm that combines multiple lines of evidence to prioritize variants and genes for further investigation.
Who developed NC-Scorer?
NC-Scorer was developed by the Halbritter Lab. The project is actively maintained and open to community contributions.
Is NC-Scorer free to use?
Yes, NC-Scorer is completely free and open-source. You can use it for academic and research purposes without any cost. The source code is available on GitHub under an MIT license.
Using NC-Scorer
How do I input a variant for scoring?
Open Score a variant on the home page, enter a variant, and select its assembly and inheritance pattern. The search forms accept:
- HGVS notation:
NM_001009944.3:c.11935C>T - VCF-style coordinates:
1-55051215-G-GAorchr1:55051215:G:GA
See Usage for segregation evidence and compound heterozygous inputs.
What do the scores mean?
NC-Scorer generates three main scores that contribute to the overall assessment:
- Gene Score (0-1): Summarizes gene evidence for kidney disease prioritization
- Variant Score (0-1): Summarizes variant annotation evidence
- Inheritance Score (0-1): Combines the selected inheritance pattern and segregation evidence
The final Nephro Candidate Score (NCS) ranges from 0-10:
- 7 ≤ NCS ≤ 10: High priority
- 3 ≤ NCS < 7: Moderate priority
- 0 ≤ NCS < 3: Low priority
The NCS is a research prioritization score, not a calibrated probability of causality.
How are scores displayed visually?
The result page presents the numeric score, its priority tier, and the three weighted components. Color helps distinguish scores; use the values and labels to interpret the result. Both light and dark themes are available.
How many variants can I process at once?
You can score up to 200 variants in one batch run. Requests are processed sequentially. Open Batch in the main menu to access this feature.
Can I save my results?
Completed individual assessments export as CSV or Excel (.xlsx). Batch results export as CSV, TSV, or JSON. See Batch Processing for the fields included in each format.
The application performs scoring in the browser and sends variant queries to external annotation services. Enabled caches store responses in browser storage.
Technical Details
What algorithms are used for scoring?
The application combines a stored gene score, a variant score calculated from CADD, gnomAD frequencies, and VEP consequence and impact annotations, and an inheritance score calculated from the selected pattern and segregation value. The combined formula is Gene × 4 + Variant × 4 + Inheritance × 2. See Scoring System for the component scales and missing-evidence rules.
Which genome builds are supported?
NC-Scorer supports both:
- GRCh37/hg19
- GRCh38/hg38 (default)
Select the assembly that matches your variant coordinates before submitting. One selected assembly applies to every variant in a batch run.
What technologies does NC-Scorer use?
NC-Scorer is built with modern web technologies:
- Frontend: Vue.js 3 with Composition API
- UI Framework: Vuetify 3 (Material Design)
- Build Tool: Vite
- State Management: Pinia
- Processing: Browser-based with API calls to specialized bioinformatics services
Is the source code available?
Yes, NC-Scorer is open-source. Visit our GitHub repository to:
- View the source code
- Report issues
- Submit pull requests
- Read contribution guidelines
Troubleshooting
My variant isn't recognized
Ensure your variant is in the correct format:
- Use standard HGVS notation (e.g., NM_033380.3:c.1871G>A)
- For genomic coordinates, specify the correct genome build
- Check that transcript IDs are valid and current
The application seems slow
NC-Scorer performs complex calculations and queries multiple databases:
- First-time queries may take several seconds
- Subsequent analyses are faster due to caching
- Enable caching through the navigation and settings menu
Why is my variant search timing out?
This can happen when:
- External APIs are temporarily unavailable
- Network connectivity issues
- Very rare or complex variants requiring extended processing
Try again after a few moments, or check your network connection.
How do I view application logs?
Click the log icon in the footer to open the log viewer. This displays:
- API requests and responses
- Processing events
- Errors and warnings
- Performance metrics
Research & Citations
How should I cite NC-Scorer?
If you use NC-Scorer in your research, please cite both our preprint publication and the software release:
Preprint Publication:
Rank N, Lukassen S, Anderegg MA, Eckardt KU, Halbritter JP, Popp B.
Automatic variant prioritization in suspected genetic kidney disease using the Nephro Candidate Score (N-CS).
medRxiv 2025. DOI: 10.1101/2025.09.29.25336840
Software Release:
NC-Scorer: Nephro Candidate Score Web Application and Framework (v3.5.4).
Release Tag: v3.5.4.
See our dedicated Citation Guide and CITATION.cff for BibTeX snippets and GitHub citation export.
Are there related publications?
The methodology behind NC-Scorer is based on the Nephro Candidate Score framework described in our medRxiv preprint (doi:10.1101/2025.09.29.25336840). Additional methodological and machine learning training details are available in the companion nephro_candidate_score repository.
Getting Help
Where can I report bugs or request features?
Please use our GitHub issue tracker to:
- Report bugs
- Suggest new features
- Ask technical questions
Before submitting, check if the issue has already been reported.
How can I contribute?
We welcome contributions! See our Contributing Guide or the CONTRIBUTING.md file for:
- Code contribution guidelines
- Development setup instructions
- Pull request process