The variant assessment tab in the CNV interpretation hub, holds comprehensive information and database summaries of the copy number region.
CNV assessment tabs is available from search query or every CNV in a case analysis.
clinical summary
This section shows the automated ACMG classification along with the most relevant genes and regions in the CNV, based on Haploinsufficiency and Triplosensitivity evidence (by Clingen and Franklin).
The most relevant syndromes will be presented, and phenotypes that match the syndrome will be highlighted.
Region viewer
Region viewer displays the genomic region information. This is a dynamic view where you can click on a cytoband and have all the relevant information:
The entire Chromosome is shown with the detailed cytobands, the borders of the CNV will be highlighted with red lines on the chromosome.
Genes in region. In large region genes details are displayed after zoom-in
Dosage sensitivity
case CNV |(sample variant)
Curated Submissions will present all the Clinvar and Decipher submissions, each line is colored by the submitted classification. A set of filters can help view variants similar to yours, for example you can filter by “Deletion” or “Duplication” and also set the “Overlap” percentage.
You can hover any submission line to see its details, a clink on the line will take you to the relevant page in Clinvar and Decipher.
Healthy population databases such as Dgv Gold, Dgv and GnomAD are also presented.
Internal Occurrence presents all the samples in your organization that have a similar CNV that overlaps by 50% or more.
Confidence (case analysis only)
Each confidence level reflects the likelihood that the CNV is real, helping users assess the reliability of the call. The confidence section visualises 3 parameters that can help assess the cnv confidence: depth, predicted copy number, and prediction scores. For more information regarding the CNV confidence view and assessment go to CNV detection by Franklin
Occurrences
the occurrences includes variants with over 50% reciprocal overlap from each database
Clinical Evidence
Clinical evidence dysplays detailed curated submissions from Clinvar, Decipher and also from Franklin community, including classification, phenotypes, % overlap, submitter, etc. each tile is expanded and includes also linkouts to the source.
Alternate Reference
The alternate reference is available for further assessment if needed, including a direct link to the variant assessment tab for the alternate allele.
Still have questions? Reach out to our Support Team, they'll be happy to help!