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Exploring the new Ensembl genome data platform - UCL Royal Free

Course Details

Lead Trainer: Jorge Batista da Rocha
Event Date: 2026-10-21
Location: London
Description: Work with the Ensembl team to get to grips with the new Ensembl browser, accessing gene, variation and genomics data.
Survey: Exploring the new Ensembl genome data platform - UCL Royal Free Feedback Survey

Materials

Demos and exercises

Introduction to the Ensembl Data Platform

Ensembl VEP

Running CFTR variants through VEP

Resequencing of the genomic region of the human CFTR (cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7) gene (ENSG00000001626) has revealed the following variants. The alleles defined in the forward strand:

G/A at 7: 117,530,985
T/C at 7: 117,531,038
T/C at 7: 117,531,068

Use the VEP tool in Ensembl and choose the options to see CADD and AlphaMissense predictions. Also enable allele frequencies from gnomAD genomes, and Phenotypes. Do these variants result in a change in the proteins encoded by any of the Ensembl genes? Which gene? Have the variants already been found in gnomAD genomes?

Go to the Ensembl homepage and click on the EnsVEP* app on the top of the page. Begin by clicking “Choose a Genome” and select Human GRCh38.p14. Then click “+” in the Variants row to add variants and paste your variants there in this format:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
117530985	var1	G	A	.	.	.
117531038	var2	T	C	.	.	.
117531068	var3	T	C	.	.	.

Note: Variation data input must be in VCF format. See more details about using VEP in the documentation page. Click Run. When your job is has finished running the Results button will becom available. click View Results.

You will get a table with the predicted consequence terms from the Sequence Ontology project (http://www.sequenceontology.org/) (i.e. synonymous, missense, downstream, intronic, 5’ UTR, 3’ UTR, etc) provided by VEP for the listed SNPs. AlphaMissense scores are available for missense SNPs only. For two of the entered positions, the variations have been predicted to have missense consequences of various pathogenicity (var2 - coordinate 117531038 and -var3 117531068), both affecting CFTR. All the three variants have been identified and have frequencies in gnomAD genomes.

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?

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.
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.