Finding a Needle in a Haystack: Variant Effect Predictor (VEP) Prioritizes Disease Causative Variants from Millions of Neutral Ones

  • Yashvant Khimsuriya
  • Salil VaniyawalaEmail author
  • Babajan BanaganapalliEmail author
  • Muhammadh Khan
  • Ramu Elango
  • Noor Ahmad ShaikEmail author


The Ensembl Variant Effect Predictor is an integrative computational platform which could provide analysis, genomic annotation, and pathogenicity predictions of genetic sequence variants lying both protein-coding and noncoding regions of the human genome. This webserver acts as a gateway to a diverse range of genomic annotations and one step platform to enter mutation data and analyze different formats of prediction outcomes. This webserver is open access and easy to use and provides reproducible results. VEP simplifies variant analysis and interpretation in diverse study settings of the human genome. This chapter describes basic navigation for VEP users and illustrates how they could use the web-based interface to analyze the single-nucleotide variants (SNVs). This includes (i) data input, (ii) pathogenicity predictions, (iii) preview of results, and (iv) downloading the results.


Variant Effect Predictor Ensembl genome browser Genomic variation SNP analysis Genotype data analysis 


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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.SN Gene Laboratory and Research CentreSuratIndia
  2. 2.Princess Al-Jawhara Center of Excellence in Research of Hereditary DisordersDepartment of Genetic Medicine, Faculty of Medicine, King Abdulaziz UniversityJeddahSaudi Arabia
  3. 3.Department of Clinical Laboratory SciencesCollege of Applied Medical Sciences, King Saud UniversityRiyadhSaudi Arabia

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