Annotators

Annotators can be divided into 2 groups:

  1. Tools that predict pathogenicity (bold)

  2. Tools that provide information like databases

  • cadd_exome (1.6.1) CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome.

  • gnomad_gene (2.2.1) Gene level population statistics from gnomAD

  • pubmed (1.1.5) articles related to a particular gene

  • clingen (1.0.1) - NIH-funded resource that defines the clinical relevance of genes and variants

  • clinpred (1.0.0) - prediction tool to identify disease-relevant nonsynonymous single nucleotide variants

  • clinvar (2021.10.01) - ClinVar is an archive of reports of the relationships among human variations and phenotypes, archive of interpretations of clinically relevant variants (Uncertain significance, Likely pathogenic, Pathogenic etc.)

  • mitomap (1.1.0) A human mitochondrial genome database

  • ncbigene (2019.08.02) - gene descriptions from NCBI (National Center for Biotechnology Information)Gene database.

  • omim (1.0.0) Catalog of human genes and genetic disorders and traits.

  • prec (3.6.0)provides a database identifying rare and likely deleterious loss-of-function (LoF) alleles

  • provean (1.0.0), tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein

  • revel (2020.12.02), ensemble method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools

  • sift (1.2.0) predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids

  • GnomADD aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects

  • PharmGKB

  • dbSNP

The most important annotators for us are ClinVar and dbSNP.