4. Data Source Version

4.1. GRCh38 (hg38)

4.1.1. Variant annotation

• star(*): the star(*) means this version is used in CGAP project.

Source name	Version	Version date	Source link
VEP *	v99	11/04/2019	➡
VEP	v100	11/04/2019	➡
dbSNP *	20190722	07/22/2019	➡
gnomAD *	3.0		➡
UK10K *	20160215	02/15/2016	➡
TOPMED *	freeze 5	08/28/2017	➡
CLINVAR *	20200106	01/06/2020	➡
COSMIC *	v90	08/06/2019	➡
SPLICEAI *	20191004	01/06/2019	➡
PRIMATEAI *	v0.2_hg38	12/18/2019	➡
CADD	1.6	03/26/2020	➡
CADD *	1.5	02/22/2019	➡
GERP *	100_mammals	01/01/2000	➡
PHASTCONS *	100way	07/17/2017	➡
PHASTCONS *	30way	07/17/2017	➡
PHASTCONS *	20way	07/17/2017	➡
PHYLOP *	100way	04/16/2015	➡
PHYLOP *	30way	11/05/2017	➡
PHYLOP *	20way	05/07/2015	➡
SIPHY *	20way	01/01/2000	➡
SUPER_DUPLICATES *	20way	01/01/2000	➡
SIMPLE_REPEAT *	20way	01/01/2000	➡
RMSK *	20way	01/01/2000	➡
NESTED_REPEATS *	20way	01/01/2000	➡
MICROSATELLITE *	20way	08/23/2015	➡

4.1.2. Gene annotation

Source name	Version	Version date	Source link
ENSEMBLgene *	v99	11/21/2019	ftp://ftp.ensembl.org/pub/release-99/gtf/homo_sapiens/Homo_sapiens.GRCh38.99.gtf.gz
ENSEMBLgene	v100	03/06/2020	ftp://ftp.ensembl.org/pub/release-100/gtf/homo_sapiens/Homo_sapiens.GRCh38.100.gtf.gz
ENSEMBLgene	v101	07/11/2020	ftp://ftp.ensembl.org/pub/release-101/gtf/homo_sapiens/Homo_sapiens.GRCh38.101.gtf.gz
ENSEMBLgeneGRCh37 *	v75(GRCh37.p13)	09/01/2013	ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz
CYTOBAND *	2017-07-17	07/17/2017	not available
CYTOBAND	2019-03-11	03/11/2019	http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cytoBand.txt.gz
RefSeq *	2020-03-20	03/20/2020	not available
RefSeq	2020-09-08	09/08/2020	ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/refseqgene.1.genomic.gbff.gz
HGNC *	2020-02-24	02/24/2020	not available
HGNC	2020-09-11	09/11/2020	ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt
ClinGen	20200403	04/03/2020	not available
ClinGen *	20200911	09/11/2020	https://search.clinicalgenome.org/kb/curations/
ClinGenDisease *	20200403	04/03/2020	not available
ClinGenDisease	20200911	09/11/2020	https://search.clinicalgenome.org/kb/gene-validity.csv
ENSEMBLIDxrefTrscriptID *	2017-11-22	11/22/2017	not available
ENSEMBLIDxrefTrscriptID	2020-08-12	08/12/2020	ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping_selected.tab.gz
ENSEMBLIDxref *	2017-11-22	11/22/2017	not available
ENSEMBLIDxref	2020-08-12	08/12/2020	ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping_selected.tab.gz
dbNSFP *	4.0c	06/05/2017	ftp://dbnsfp:dbnsfp@dbnsfp.softgenetics.com/dbNSFP4.0c.zip
gnomADmetrics *	v2.1.1	11/22/2017	https://storage.googleapis.com/gnomad-public/release/2.1.1/constraint/gnomad.v2.1.1.lof_metrics.by_gene.txt.bgz
Marrvel *	v1.2	06/01/2017	http://marrvel.org/doc
CassaNatGenet2017 *	04/03/2017	04/03/2017	https://www.biorxiv.org/highwire/filestream/20869/field_highwire_adjunct_files/0/075523-1.xlsx
GTEx *	v8	06/05/2017	https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct.gz
BrainSpan *	v2	06/05/2017	not available
BrainSpan	v10	06/05/2017	https://www.brainspan.org/api/v2/well_known_file_download/267666525
BrainAtlas *	v2	03/01/2013	https://human.brain-map.org/api/v2/well_known_file_download/178238359
GenCode *	v33	12/13/2019	ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_33/gencode.v33.annotation.gff3.gz
GenCode	v35	03/01/2020	ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_35/gencode.v35.annotation.gff3.gz

4.2. GRCh37 (hg19)

4.2.1. Variant annotation

Source name	Version	Date	link
CADD	1.6	03/26/2020	➡

4.2.2. Gene annotation