Table 3.

Biological classification (variant level) KBs. In addition to the technical parameters and survey responses as introduced in Table 2, we report whether a KB contains information on somatic variants and/or germline variants as well as pre-computed functional prediction scores. We do not apply the somatic/germline distinction when databases provide functional prediction results only. Note that germline variants in cBioPortal are not publicly available. Further, note that in the included population/healthy controls data sets (ExAC, 1000 Genomes Project, EVS, DGV and PGP), somatic variants may be found occasionally; therefore, the column is checked in parentheses.

Database	Source	Survey	Acad. use	API	Dump	Update interval	Somatic variants	Germline variants	Prediction scores
COSMIC	[72]	100%	✓	✓	✓	3 m	✓
ClinVar	[73]	100%	✓	✓	✓	1 w	✓	✓
cBioPortal	[74]	90%	✓	✓	✓	1 w–1 m*	✓	(✓)
dbSNP	[75]	60%	✓	✓	✓	Upon submission	✓	✓
ExAC	[76]	60%	✓	–	✓	–	(✓)	✓
OMIM	[77]	60%	✓	✓	✓	1 d	✓	✓
HGMD	[78]	60%	✓	–	(✓)	3 m		✓
gnomAD	[79]	50%	✓	–	✓	Last: October 2020	(✓)	✓
LOVD	[80]	50%	✓	✓	✓	6 m	✓	✓
1000 Genomes Project	[81]	40%	✓	✓	✓	Last: May 2013	(✓)	✓
CADD	[82]	40%	✓	✓	✓	1 y	–	–	✓
BRCA Exchange	[83]	40%	✓	✓	✓	2 m		✓
EVS	[84]	40%	✓	–	✓	Unknown	(✓)	✓	✓
Cancer Gene Census	[85]	30%	✓	–	✓	3 m	✓	✓
IARC WHO TP53 Mutation Database	[86]	30%	✓	–	✓	1 y	✓	✓	✓
Mastermind	[87]	30%	(✓)	(✓)	–	–	✓	✓
UMD	[88]	30%	✓	–	✓	Last: January 2013		✓
dbNSFP	[54]	20%	✓	–	✓	3–6 m	–	–	✓
ClinGen	[89]	10%	✓	✓	–	–		✓
DGV	[90]	10%	✓	–	✓	1–4 y	(✓)	✓
dbVar	[91]	10%	✓	✓	✓	1–2 m	✓	✓
DoCM	[92]	0%	✓	✓	–	–	✓
Intogen	[93]	0%	✓	–	✓	Last: February 2020	✓
PGP	[94]	0%	✓	–	✓	Upon submission	(✓)	✓