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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.

Paste 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.