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VEP analysis of structural variants in human

We have details of a genomic deletion in a breast cancer sample in VCF format:

13 32307062 sv1 . <DEL> . . SVTYPE=DEL;END=32908738

Use VEP in Ensembl to find out the following information:

1.  How many genes have been affected?

2.  Does the structural variant (SV) cause deletion of any complete transcripts?

3.  Map your variant in the Ensembl browser on the Region in detail view.

  1. Click on VEP at the top of any Ensembl page and open the web interface. Make sure your species is Human. It is good practise to name your VEP jobs something descriptive, such as Patient deletion exercise. Paste the variant in VCF format into the Paste data field and hit Run.

    12 different genes are affected by the SV.

  2. Filter your table by select Consequence is transcript_ablation at the top of the table and click Add.

    Yes, there is deletion of complete transcripts of PDS5B, N4BP2L1, BRCA2, RNY1P4, IFIT1P1, ATP8A2P2, N4BP2L2, N4BP2L2-IT2 and three genes without official symbols: ENSG00000212293, ENSG00000270008 and ENSG00000277151.

  3. 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 the Personal data tab in the pop-up menu.