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Table 1 Source datasets used for annotation

From: cnvScan: a CNV screening and annotation tool to improve the clinical utility of computational CNV prediction from exome sequencing data

Source Extracted information Reference
Gene and functional effect datasets
 Gencode V.19 Gene name (HGNC gene symbol)
Gene type
Gene IDs (Ensemble)
Transcript IDs (Ensemble)
Exon counts (Internal to CNVs)
 PhastCon PhastCon element count
PhastCon element score
Haploinsufficiency index Haploinsufficiency score
 Gene intolerance Gene intolerance score
Known CNVs
 Sanger high resolution CNVs Sanger CNV count
 DGV DGV CNV count
Variant type
Variant subtype
Pubmed ID
 Curated high quality DGV CNVs from 2 stringency levels
CNV population frequencies
 1000 Genomes CNVs 1000 Genomes deletion
1000 Genomes insertions
Clinically relevant information
 OMIM morbid map OMIM disease
Pubmed ID
 DECIPHER DECIPHER development disorder genes
 ClinVar ClinVar disease
HGVS name of the variant