Copy number

Copy-number variants (CNVs) are changes in the number of copies of a region: losses (deletions) and gains (duplications). The Copy Number tab presents the CNV calls with visualizations built for dosage review.

Visualizations

• Scatter plot: a genome-wide view of the copy-number calls.

• Ideogram: the calls arranged across the chromosomes. Click directly on the visualization to open a slide-out panel for the selected gene.

Calls are colour-coded for deletions and duplications, and for their classification (likely pathogenic, uncertain, or likely benign).

A gene dosage matrix is also part of this tab. It does not yet have a visualization; this page will be updated when it ships.

The candidate table

Each row is a genotyped copy-number variant. You can search, sort, filter, and customize the columns in the table using the Columns dropdown.

The default columns in the candidate table include:

Column	Description
User Classification	The classification manually assigned to the copy-number variant by a reviewer (e.g., Pathogenic, Likely Pathogenic, VUS, Benign).
Automated Classification	The automated classification generated by the system's pipeline rules or algorithms.
AnnotSV Score	The pathogenicity annotation score or class assigned by AnnotSV.
SV Type	The type of copy-number variant (e.g., DEL (deletion/loss), DUP (duplication/gain)).
Chrom	The chromosome where the copy-number variant is located.
Pos	The starting genomic coordinate of the copy-number variant.
End Position	The ending genomic coordinate of the copy-number variant.
Genes	Standard gene symbols of the genes overlapped or affected by the copy-number variant.
SV Length	The length of the copy-number variant in base pairs.
Filter Status	The filter status of the variant call from the caller (e.g., PASS or specific filtering flags).

Filters

The filter drawer offers:

• User Classification: Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign.

• Type: DEL (loss) or DUP (gain).

• Gene: filter by gene symbol.

• Chromosome: chr1 to chr22, chrX, chrY.

• Copy Number: an integer copy-number range.

• Position: a genomic-coordinate range.

How to review

1. Scan the scatter and ideogram views for calls flagged as likely pathogenic.

2. Click a call to open its detail panel and review the affected genes and dosage change (loss vs gain).

3. Classify and add findings to the report.