Ensembl Home
More ▼
Ensembl VEP analysis of structural variants in human

<- Back to exercise page

Ensembl 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?

  1. Click on EnsVEP at the top of any Ensembl page. Make sure your species is Human GRCh38. It is good practise to name your VEP jobs something descriptive, such as Patient deletion exercise. Paste the variant in VCF format into the Variants field, select any options and hit Run.

    7 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, IFIT1P1, ATP8A2P2, N4BP2L2.