Data sources

At GeneBe, we believe that providing accurate and up-to-date information is crucial for our users. That's why we continuously update our data sources to ensure that we provide the latest and most reliable information possible. Below is a list of the data sources we currently use to provide our users with the most comprehensive and accurate information.

Please note that the list provided below is not comprehensive and is subject to change. We are continuously adding new data sources to our platform, and some of the sources we use are not yet listed here. We apologize for any inconvenience this may cause, and we are working to update the list regularly.

Pathogenicity Scores and Related Resources

Name	Comment	Note	Link
AlphaMissense	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/37733863
Apogee2	Pathogenicity score for mitochondria		https://pubmed.ncbi.nlm.nih.gov/37598215
BayesDel_noAF	Pathogenicity score, precomputed for whole genome		https://pubmed.ncbi.nlm.nih.gov/27995669
CADD	Pathogenicity score, precomputed for whole genome	freely available only for non-commercial use	https://pubmed.ncbi.nlm.nih.gov/24487276
CardioBoost	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/33046849/
ClinVar	Reputable source of variant pathogenicity		https://pubmed.ncbi.nlm.nih.gov/29165669/
Dann	Precomputed for whole genome		https://pubmed.ncbi.nlm.nih.gov/25338716/
dbscSNV1_ADA	Pathogenicity score for splicing		https://pubmed.ncbi.nlm.nih.gov/25416802/
dbscSNV1_RF	Pathogenicity score for splicing		https://pubmed.ncbi.nlm.nih.gov/25416802/
Deogen2	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/28498993
Domino	Gene annotation data		https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5630195/
SpliceAI	Pathogenicity score for splicing		https://pubmed.ncbi.nlm.nih.gov/30661751
Fathmm_mkl	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/23033316
gMVP	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/25552646/
GERP	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/15965027/
GeneCC	Gene annotation data		https://thegencc.org/
Gnomad exome	Population allele frequency source		https://pubmed.ncbi.nlm.nih.gov/32461654/
Gnomad genome	Population allele frequency source		https://pubmed.ncbi.nlm.nih.gov/32461654/
Gnomad mito	Population allele frequency source		https://pubmed.ncbi.nlm.nih.gov/32461654/
HmtVar	Pathogenicity score for mitochondria		https://pubmed.ncbi.nlm.nih.gov/30371888
ListS2	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/32352516
LOVD	Reputable source of variant pathogenicity		https://pubmed.ncbi.nlm.nih.gov/21520333/
LRT	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/19602639
MaxEntScore	We use our implementation.		https://pubmed.ncbi.nlm.nih.gov/15285897/
mCAP	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/27776117
MetaLR	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/25552646
MetaRNN	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/36209109/
MetaSVN	Pathogenicity score		https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4375422/
Mitotip	Pathogenicity score for mitochondria		https://pubmed.ncbi.nlm.nih.gov/29227991
Mitomap	Population allele frequency source		https://pubmed.ncbi.nlm.nih.gov/25489354
MPC	Pathogenicity score		https://doi.org/10.1101/148353
MutationAssessor	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/21727090
MutationTaster	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/24681721
MutPred	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/19734154
PhyploP100_way_vertebrate	Conservation score		https://pubmed.ncbi.nlm.nih.gov/16024819/
Polyphen	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/20354512
PrimateAI	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/30038395
PROVEAN	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/23056405
REVEL	Pathogenicity score		https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5065685/
Sift	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/26633127
SnpEff	Variant consequence predictor		https://pubmed.ncbi.nlm.nih.gov/22728672
Topmed	Population allele frequency source		https://bravo.sph.umich.edu/
UniProt	Pathogenicity score		https://pubmed.ncbi.nlm.nih.gov/30395287/
VEP	Variant consequence predictor		https://pubmed.ncbi.nlm.nih.gov/27268795/
Varity_R	Pathogenicity score		https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8546039/

Some of scores are imported from dbNSFP database https://pubmed.ncbi.nlm.nih.gov/33261662/

Presented list is not exhaustive, as it is continuously expanding with new sources being added constantly.