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  • Variant Effect Predictor
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Variant Effect Predictor

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This component determines the effect of genetic variants using Ensembl's Variant Effect Predictor (VEP) via their REST API (https://rest.ensembl.org/#VEP). The output table contains the most severe predicted effect of the variant and the associated gene symbol. In addition, the minor allele frequency from the 1000 genomes project, frequency information from the Genome Aggregation Database (gnomAD), and the SIFT score are extracted (if available). The SIFT Score indicates whether an amino acid substitution affects protein function (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC168916/), it ranges from 0 to 1, with low scores indicating a damaging effect. Those effects are calculated per transcript, therefore transcript information (Ensembl ID) is included as well. In the interactive view the user can filter variants by minor allele frequencies and SIFT score and select variants of interest. If nothing is selected all data will be available at the output port. The view also contains an explanatory image of the variant consequences taken from http://www.ensembl.info/2012/08/06/variation-consequences/.

Component details

Input ports
  1. Type: Table
    Input table with variants.
Output ports
  1. Type: Table
    Output table containing the most severe consequence of the variant, variant frequencies from the 1000 genomes project and gnomAD, and the SIFT score.

Used extensions & nodes

Created with KNIME Analytics Platform version 4.3.0
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    KNIME Base nodes Trusted extension

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    Version 4.3.0

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    KNIME Expressions Trusted extension

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    Version 4.3.0

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    KNIME JavaScript Views Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.3.0

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    KNIME Javasnippet Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.3.0

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    KNIME Math Expression (JEP) Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.3.0

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    KNIME Quick Forms Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.3.0

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    KNIME REST Client Extension Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.3.0

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    KNIME XML-Processing Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.3.0

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Legal

By using or downloading the component, you agree to our terms and conditions.

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