Table 1. Different annotations available within VarAFT and their availability for filtration.
| LEVEL | ANNOTATION | FILTRATION |
|---|---|---|
| VARIANT | Localization | |
| RefGene (Gene, Transcript, Function, Nomenclature) | X | |
| Ensembl (Gene, Transcript, Function, Nomenclature) | X | |
| Frequency | ||
| 1000 Genomes | X | |
| DbSNP | X | |
| Genome Aggregation Database (gnomAD) | X | |
| Known VARiants (KaViar) | X | |
| Haplotype Reference Consortium (HRCR1) | X | |
| Great Middle East Database (GME) | X | |
| Prediction | ||
| UMD-Predictor | X | |
| Human Splicing Finder | X | |
| SIFT | X | |
| Polyphen 2 | X | |
| LRT | X | |
| Mutation Taster | X | |
| Mutation Assessor | X | |
| FATHMM | ||
| PROVEAN | X | |
| VEST3 | ||
| MetaSVM | ||
| MetaLR | ||
| M-CAP | X | |
| CADD | X | |
| DANN | X | |
| FATHMM-MKL | ||
| Eigen | X | |
| GERP++ | X | |
| Conservation | ||
| phyloP100way | ||
| phyloP20way | ||
| phastCons100way | ||
| phastCons20way | ||
| SiPhy_29way | ||
| wgRNA | ||
| predicted microRNA targets (target ScanS) | ||
| genomicSuperDups | ||
| gwasCatalog | ||
| wgEncodeBroadHmmGm12878HMM | ||
| GENE | Expression | |
| GTEx | X | |
| Pathways/GO | ||
| KEGG | X | |
| Pathway Interactome Database (PID) | X | |
| REACTOME | X | |
| Gene Ontology | X | |
| Score Tolerance | ||
| Residual Variation Intolerance Score (RVIS) | X | |
| Gene Damaging Index (GDI) | X | |
| Lost Of Function Tool (LOF) | X | |
| genome-wide haploinsufficiency score (GHIS) | X | |
| DISEASE PHENOTYPE | Ontology | |
| Human Phenotype Ontology (HPO) | X | |
| Database | ||
| Online Mendelian Inheritance in Man (OMIM) | X | |
| Catalogue Of Somatic Mutations In Cancer (Cosmic) | X | |
| ClinVar | X | |
X = annotation available for filtration.