Visualizing CNVs in VarSome

The VarSome v10.3 release provides the functionality for viewing CNVs in VarSome and VarSome Premium.

Example CNVs have been provided in both the drop down menu from the search bar and in the  examples page:

VarSome CNV nomenclature

In VarSome, CNVs are encoded in a colon separated, four field format:

<chromosome>:<start coordinate>:<L|E><end coordinate>:<DUP|DEL>

Field 1 - chromosome: chromosome in UCSC format, for example “chr1”, “chr9”, “chrX”, etc.

Field 2 - start coordinate: genomic coordinate denoting the start position of the CNV. 

Field 3 - end coordinate/length: If preceded by “E” or “e” (end), the coordinate denotes the end position of the CNV. If preceded by an “L” or “l” (length), then it denotes the length of the CNV. If there is no preceding flag, then “E” is implied.

Field 4 - copy number variation type. Value can be “DUP” for duplications or “DEL” for deletions. Please use CAPS only.

Examples

hg19 reference genome

chr7:117138367:117159446:DEL

A Pathogenic 21,079bp long deletion spanning exons 1 and 2 of CFTR

chr3:37039445:37059613:DUP

A 20,168 Likely Pathogenic duplication spanning exons 3-10 of MLH1

chr21:36160098:36171759:DEL

A 11,661 Pathogenic deletion spanning the final two exons of the RUNX1 transcript

chr1:110230496:110235917:DUP

A 5,421 Benign duplication spanning genes GSTM1 and GSTM2

chr2:97854824:97855027:DUP

A 203bp duplication of Uncertain Significance spanning parts of exons 33 and 34 of ANKRD3 

hg38 reference genome

chr17:43098764:43110978:DEL

A 12,214 Pathogenic deletion of exons 4-7 of BRCA1

chr13:32317656:32331987:DUP

A 4,331bp Likely Pathogenic duplication of exon 3 of BRCA2

8:127734450:127764981:DUP

A 30,531bp duplication of Uncertain Significance spanning MYC

chr1:13308329:13308887:DEL

A 558bp Benign deletion of large part of exon 4 of PRAMEF4

Coding and non coding genes within the CNV region are displayed in tables: 

A Maximum of 15 coding genes are listed as links in the right hand menu:

An ACMG CNV Classification is provided showing triggered rules: 

We also provide a structural variant browser for CNVs retrieved from CNV databases:

Publications related to the genomic region spanned by the CNV are retrieved and displayed in the Publications section. Relevant publications are sourced from Clinvar CNV, UniProt regions, DECIPHER, GnomAD and DBVAR databases. In addition, the user can access gene associated publications by clicking on the right hand menu, where all genes overlapping the CNV are listed. Clicking on any of these genes will link to VarSome gene view containing related publications:

We also display a list of transcripts associated associated with this CNV: 

Further Information and Support

Not already a VarSome Premium user? Get in touch and ask for a free trial.

As ever we hope you find these changes and improvements helpful, we’d love to hear any suggestions you may have, support is available as usual from support@varsome.com

- The VarSome Team