Variant Effect Predictor

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/.

Options

Select column with variants (Genomic Region, HGVS Nomenclature, or reference SNP ID)

The variants can be in HGVS notation (for example AGT:c.803T>C), as reference SNP ID (for example rs56116432) or genomic region (for example 1:156232382-156232382:1/G).

Identifier

Select identifier for which variant consequences should be fetched%%00010This can be Genomic Region, HGVS Nomenclature, or reference SNP ID. %%00010%%00010For more information see https://www.ncbi.nlm.nih.gov/books/NBK44417/#Content.what_is_a_reference_snp_or__rs_i on rs id and http://varnomen.hgvs.org/ on the HGVS notation.

Nodes

• Range Slider Filter Definition3 ×
• Row Filter3 ×
• Breakpoint2 ×
• Column Expressions2 ×
• CASE Switch Data (Start)1 ×
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Extensions

• FeatureKNIME Base nodes
• FeatureKNIME Column Expressions (legacy)
• FeatureKNIME JavaScript Views
• FeatureKNIME Javasnippet
• FeatureKNIME Math Expression (JEP)
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