The Ensembl Variant Effect Predictor (VEP) is a powerful tool for analyzing, annotating, and prioritizing genomic variants in coding and non-coding regions. It provides extensive genomic annotation with various interfaces and allows for configuration and extension of analysis. The VEP is open-source, free to use, and ensures full reproducibility of results. It simplifies and accelerates variant interpretation in various study designs. The VEP is used for analyzing traits in farm animals, patient diagnosis, and research on genome-wide association studies (GWAS). It has been used in large-scale projects such as the 1000 Genomes and Exome Aggregation Consortium (ExAC). VEP annotations are used as input for tools like GEMINI for deep exploration of variant annotation. It is a flexible tool for detailed sequence variant annotation. The VEP annotates two broad categories of genomic variants: (1) sequence variants with specific changes, including SNVs, insertions, deletions, and microsatellites; and (2) larger structural variants. It provides detailed annotation for effects on transcripts, proteins, and regulatory regions, including allele frequencies and disease information. The VEP supports input data in variant call format (VCF) and can process variant identifiers and HGVS nomenclature. It outputs results in HTML, text, tab-delimited, VCF, GVF, or JSON formats. The VEP has an online interface, a Perl script, and a REST API. It is platform-independent and can be used for both small and large datasets. The VEP provides detailed annotations for gene and transcript-related information, protein sequence changes, and non-coding regions. It includes frequency, phenotype, and citation annotations, as well as plugins for additional analysis. The VEP supports multiple species and provides flexible "plugin" architecture for algorithmic extensions. The VEP is used for variant analysis in various species, including humans, mice, and other organisms. It supports both the latest GRCh38 and previous GRCh37 human assemblies. The VEP is open-source, free to use, and actively maintained. It is used in research and clinical settings for variant interpretation and prioritization. The VEP is efficient and can process large datasets quickly. It is compared with other tools like Annovar and SnpEff, showing similar or faster performance. The VEP provides standardized variant annotation terms and supports various formats for output. It is used in genome-wide studies and has potential for future improvements in variant interpretation.The Ensembl Variant Effect Predictor (VEP) is a powerful tool for analyzing, annotating, and prioritizing genomic variants in coding and non-coding regions. It provides extensive genomic annotation with various interfaces and allows for configuration and extension of analysis. The VEP is open-source, free to use, and ensures full reproducibility of results. It simplifies and accelerates variant interpretation in various study designs. The VEP is used for analyzing traits in farm animals, patient diagnosis, and research on genome-wide association studies (GWAS). It has been used in large-scale projects such as the 1000 Genomes and Exome Aggregation Consortium (ExAC). VEP annotations are used as input for tools like GEMINI for deep exploration of variant annotation. It is a flexible tool for detailed sequence variant annotation. The VEP annotates two broad categories of genomic variants: (1) sequence variants with specific changes, including SNVs, insertions, deletions, and microsatellites; and (2) larger structural variants. It provides detailed annotation for effects on transcripts, proteins, and regulatory regions, including allele frequencies and disease information. The VEP supports input data in variant call format (VCF) and can process variant identifiers and HGVS nomenclature. It outputs results in HTML, text, tab-delimited, VCF, GVF, or JSON formats. The VEP has an online interface, a Perl script, and a REST API. It is platform-independent and can be used for both small and large datasets. The VEP provides detailed annotations for gene and transcript-related information, protein sequence changes, and non-coding regions. It includes frequency, phenotype, and citation annotations, as well as plugins for additional analysis. The VEP supports multiple species and provides flexible "plugin" architecture for algorithmic extensions. The VEP is used for variant analysis in various species, including humans, mice, and other organisms. It supports both the latest GRCh38 and previous GRCh37 human assemblies. The VEP is open-source, free to use, and actively maintained. It is used in research and clinical settings for variant interpretation and prioritization. The VEP is efficient and can process large datasets quickly. It is compared with other tools like Annovar and SnpEff, showing similar or faster performance. The VEP provides standardized variant annotation terms and supports various formats for output. It is used in genome-wide studies and has potential for future improvements in variant interpretation.