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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

NameCommentPublication or link
AlphaMissensePathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/37733863
Apogee2Pathogenicity score for mitochondriahttps://pubmed.ncbi.nlm.nih.gov/37598215
BayesDel_noAFPathogenicity score, precomputed for whole genomehttps://pubmed.ncbi.nlm.nih.gov/27995669
CADDPathogenicity score, precomputed for whole genomehttps://pubmed.ncbi.nlm.nih.gov/24487276
CardioBoostPathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/33046849/
ClinVarReputable source of variant pathogenicityhttps://pubmed.ncbi.nlm.nih.gov/29165669/
DannPrecomputed for whole genomehttps://pubmed.ncbi.nlm.nih.gov/25338716/
dbscSNV1_ADAPathogenicity score for splicinghttps://pubmed.ncbi.nlm.nih.gov/25416802/
dbscSNV1_RFPathogenicity score for splicinghttps://pubmed.ncbi.nlm.nih.gov/25416802/
Deogen2Pathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/28498993
DominoGene annotation datahttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5630195/
SpliceAIPathogenicity score for splicinghttps://pubmed.ncbi.nlm.nih.gov/30661751
Fathmm_mklPathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/23033316
gMVPPathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/25552646/
GERPPathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/15965027/
GeneCCGene annotation datahttps://thegencc.org/
Gnomad exomePopulation allele frequency sourcehttps://pubmed.ncbi.nlm.nih.gov/32461654/
Gnomad genomePopulation allele frequency sourcehttps://pubmed.ncbi.nlm.nih.gov/32461654/
Gnomad mitoPopulation allele frequency sourcehttps://pubmed.ncbi.nlm.nih.gov/32461654/
HmtVarPathogenicity score for mitochondriahttps://pubmed.ncbi.nlm.nih.gov/30371888
ListS2Pathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/32352516
LOVDReputable source of variant pathogenicityhttps://pubmed.ncbi.nlm.nih.gov/21520333/
LRTPathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/19602639
MaxEntScoreWe use our implementation.https://pubmed.ncbi.nlm.nih.gov/15285897/
mCAPPathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/27776117
MetaLRPathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/25552646
MetaRNNPathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/36209109/
MetaSVNPathogenicity scorehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4375422/
MitotipPathogenicity score for mitochondriahttps://pubmed.ncbi.nlm.nih.gov/29227991
MitomapPopulation allele frequency sourcehttps://pubmed.ncbi.nlm.nih.gov/25489354
MPCPathogenicity scorehttps://doi.org/10.1101/148353
MutationAssessorPathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/21727090
MutationTasterPathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/24681721
MutPredPathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/19734154
PhyploP100_way_vertebrateConservation scorehttps://pubmed.ncbi.nlm.nih.gov/16024819/
PolyphenPathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/20354512
PrimateAIPathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/30038395
PROVEANPathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/23056405
REVELPathogenicity scorehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5065685/
SiftPathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/26633127
SnpEffVariant consequence predictorhttps://pubmed.ncbi.nlm.nih.gov/22728672
TopmedPopulation allele frequency sourcehttps://bravo.sph.umich.edu/
UniProtPathogenicity scorehttps://pubmed.ncbi.nlm.nih.gov/30395287/
VEPVariant consequence predictorhttps://pubmed.ncbi.nlm.nih.gov/27268795/
Varity_RPathogenicity scorehttps://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.