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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Single Nucleotide Polymorphisms-SNPs01:05

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Updated: Oct 12, 2025

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor-A tutorial.

Sarah E Hunt1, Benjamin Moore1, Ridwan M Amode1

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.

Human Mutation
|November 24, 2021
PubMed
Summary
This summary is machine-generated.

The Ensembl Variant Effect Predictor (VEP) tool annotates and filters genomic variants. This open-source software aids researchers in understanding variant impacts using multiple databases and prediction tools.

Keywords:
VEPfilteringvariant annotationvariant prioritisation“molecular consequence”

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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genomic variant annotation is crucial for understanding molecular consequences and disease associations.
  • Existing tools require significant bioinformatics expertise, limiting accessibility.
  • The Ensembl Variant Effect Predictor (VEP) offers a comprehensive solution for variant analysis.

Purpose of the Study:

  • To describe the functionality and usage of the Ensembl Variant Effect Predictor (VEP) tool.
  • To provide a tutorial on performing variant annotation using the VEP web interface.
  • To highlight VEP's capabilities in predicting molecular consequences, phenotype associations, and deleteriousness.

Main Methods:

  • Utilizing the Ensembl/GENCODE or RefSeq gene sets for variant consequence prediction.
  • Integrating data from ClinVar for phenotype associations and gnomAD for allele frequencies.
  • Employing deleteriousness prediction tools like Sorting Intolerant From Tolerant (SIFT) and Combined Annotation Dependent Depletion (CADD).
  • Leveraging VEP's filtering options for variant prioritization.
  • Performing analysis via command-line tool, REST API, or web interface.

Main Results:

  • Ensembl VEP accurately predicts molecular consequences of genomic variants.
  • It integrates diverse data sources, including phenotype and allele frequency information.
  • The tool offers flexible analysis methods suitable for various user needs and expertise levels.
  • The web tool provides a user-friendly interface for sophisticated variant annotation.

Conclusions:

  • Ensembl VEP is a powerful, versatile, and accessible tool for genomic variant annotation and filtering.
  • Its regular updates ensure incorporation of the latest biological and variant data.
  • The availability of multiple access methods enhances its utility across different research settings.
  • The VEP web tool simplifies complex variant analysis for a broader scientific audience.