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ClinVar: variant-level clinical classification
InvitaeKB: variant-level clinical classification based on Sherloc and expert manual curation available for GRCh37 samples (Nykamp et al., 2017)
Snpeff: variant effect annotation (using Ensembl 37.75, 38.86 as reference for the respective genome builds)
dbNSFP: in silico conservation and prediction scores
EVE: in silico prediction score based on a computational method trained solely on evolutionary sequences (Frazer et al., 2021)
dbscSNV: splice site prediction scores for splice region variants, defined as position located −3 to +8 at the 5’ splice site and −12 to +2 at the 3’ splice site” (Jian et al., 2014).
SpliceAI: splice prediction scores annotated for SNVs and 1-2 nt sized indels located in exonic regions of Apollo genes, or within 200 nt flanking intronic regions (Jaganathan et al., 2019)
Apollo (by Invitae): disorder-related annotations including disease name, associated genes, overlap with the input phenotype, inheritance pattern, age of onset etc.
Ensembl: 37.75, 38.86 as reference for the respective genome builds
RefSeq: transcript ID annotation. Translation of ENST into RefSeq provided by Ensembl.
gnomAD: population allele frequencies for single nucleotide variants
gnomAD_MT: population allele frequencies for mitochondrial variants
gnomAD_SV: population allele frequencies for annotation of deletions and duplications
HPO: Human phenotype ontology terms
DGV: population allele frequencies for annotation of deletions and duplications (DGV Gold standard; http://dgv.tcag.ca/ Database of Genomic Variants)
dbVar: Structural Variants with clinical assertions
Mitomap: GenBank variant frequencies
Mitimpact: in silico conservation and prediction scores of mitochondrial variants
Mastermind: Cited Variants Reference linking genetic variants to medical literature (https://www.genomenon.com/cvr/ Mastermind Cited Variants Reference)
CaseRepoSample: Sample observations, based on samples uploaded in your lab account, annotated as ‘Lab frequency’ for each variant.
ClinGen regions: Curated dosage sensitive regions
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