Viewing structural variants with the VEP
We have details of a genomic deletion in a breast cancer sample in VCF format:
13 32307062 sv1 . <DEL> . . SVTYPE=DEL;END=32908738
(a) How many genes have been affected?
(b) Does the SV cause deletion of any complete transcripts?
(c) Display your variant in the Ensembl browser.
(a) Give your data a name, such as Patient deletion.
13 32307062 sv1 . <DEL> . . SVTYPE=DEL;END=32908738 into the Paste data field then hit Run.
13 genes have been affected.
(b) Use the Filters, selecting Consequence is transcript_ablation, Add.
Yes, there is deletion of complete transcripts of PDS5B, N4BP2L1, BRCA2, RNY1P4, IFIT1P1, ATP8A2P2, N4BP2L2, N4BP2L2-IT2, AL137247.1, AL137247.2 and AL138820.1.
(c) To view your variant in the browser click on the location link in the results table 13: 32307062-32908738. The link will open the Region in detail view in a new tab. If you have given your data a name it will appear automatically in red. If not, you may need to Configure this page and add it under Personal Data.