Usage

Open the NC-Scorer application, or use the local address printed by npm run dev. The home page has three search tabs: Score a variant, Variant details, and Find a gene.

Score a variant

1. Enter a variant in VCF-style notation, such as 1-55051215-G-GA, or HGVS notation, such as NM_001009944.3:c.11935C>T.
2. Choose the genome assembly: GRCh38 / hg38 or GRCh37 / hg19. It must match your variant coordinates.
3. Select the inheritance pattern. For compound heterozygous analysis, enter the required second variant.
4. If a segregation field appears, enter a value from 0 to 1, or leave it blank when unknown.
5. Select Calculate score, then review the gene, variant, and inheritance evidence alongside the combined score.

The example links open assessments with their listed inheritance and assembly settings. Use Edit Search on the result page to return to the form with your current inputs.

Segregation evidence

The calculation treats the segregation value as a p-value: smaller values increase the inheritance score. Zero is a valid supplied value. Leaving the field blank applies a 0.8 multiplier to the inheritance score when that inheritance pattern expects segregation evidence. This is a 20% reduction of the inheritance component, not of the combined NCS.

The form hides segregation for Denovo, Unknown, and Compound heterozygous (suspected); these patterns do not receive a missing-segregation penalty.

Variant details

Use Variant details to enter a VCF-style or HGVS identifier and choose its assembly. Select Look up variant to inspect variant annotations, population frequencies, scores, and transcript details. This view does not collect the inheritance evidence needed for a combined NCS.

Find a gene

Use Find a gene to enter a symbol such as PKD1 or COL4A5, or an HGNC identifier such as HGNC:9008 or 9008. Choose an autocomplete suggestion or select Look up gene. The result shows gene evidence and its gene score. The Genes navigation item opens the gene-score table.

Understanding the result

Each component is on a 0–1 scale. The combined score is on a 0–10 scale:

NCS = (Gene Score × 4) + (Variant Score × 4) + (Inheritance Score × 2)

The gene component uses the stored gene score. The variant component uses CADD, gnomAD population frequencies, and VEP consequence and impact annotations. The inheritance component uses the selected pattern and segregation evidence.

Combined NCS	Priority
0 ≤ NCS < 3	Low
3 ≤ NCS < 7	Moderate
7 ≤ NCS ≤ 10	High

These tiers support research prioritization. A completed score requires all three component scores; an unavailable or failed response should be reviewed before proceeding. See Scoring System for the calculation details.

Export and batch work

When a combined assessment is complete, its Download menu provides CSV and Excel (.xlsx) exports with the score breakdown and available supporting details.

For lists of up to 200 variants, open Batch. Batch results have separate CSV, TSV, and JSON download options. See Batch Processing for input formatting and export contents.

Display and settings

Use the sun or moon button to change theme. The navigation and settings menu includes the API cache toggle, a guided tour, and a citation-copy action. Caching can speed up repeated lookups; disable it when you need fresh API responses.