Rebuilt variant set for all possible nsSNVs and ssSNVs based on latest GENCODE release 48 (Ensembl v114).
Added MutPred2 to replace MutPred v1.2 scores, included in both a and c branch (Thanks to Drs. Timothy Bergquist and Vikas Pejaver from MSMU).
Updated ESM1b scores to include more missense mutations (Thanks to Drs. Po-Yu Lin and Nadav Brandes from NYU).
Added GenCC gene annotations.
Updated following resources to their current versions: ancestral alleles, ClinVar, dbSNP, GWAS catalog, InterPro, ClinGen, Gene Ontology, HGNC, HPO, IntAct, MGI, OMIM, UniProt, RefSeq and ZFIN.
Rebuilt variant set for all possible nsSNVs and ssSNVs based on latest GENCODE release 47 (Ensembl v113).
Added Allele frequencies from All of Us (250k genomes) and Regeneron Genetics Center Million Exome (RGC-ME) (Thanks to Moez Dawood and Dr. Richard Gibbs from HGSC at Baylor College of Medicine).
Added dbNSFP_POPMAX_AF/AC etc. based on all population allele frequency columns curated in dbNSFP.
Updated MutationTaster2021 to include more missense mutations (Thanks to Franziska Fritz and Dr. Dominik Seelow from Berlin Institute of Health).
Other updated resources include Clinvar, GWAS catalog, OMIM, Orphanet, ClinGen Dosage Sensitivity, Interpro, HGNC, Uniprot, IntAct, Gene Ontology, MGI, ZFIN, UniParc, RefSeq, MANE, and HPO.
Provided dbNSFP files in a format ready to use with Ensembl Variant Effect Predictor (VEP) (Thanks to Dr. Jamie Allen from EMBL-EBI) and SnpSift.
Fully rebuilt based on GENCODE release 46/Ensembl 112
Transcripts annotations from the MANE project has been added.
Allele frequencies from TOPMed freeze8, and gnomAD exome controls, non-neuro, and non-cancer subsets from v2.1.1 have been added.
Allele frequencies from gnomAD have been updated to v4.1 joint data set (genome+exome).
bStatistic, ancestral alleles, and ClinVar have been updated.
MutationTaster has been updated to MutationTaster2021.
The gene table has also been rebuilt. ClinGen Dosage Sensitivity and Humnan Protein Atlas consensus gene expression levels have been added.
HGNC, Uniprot, IntAct, GWAS catalog, Interpro, Gene Ontology, ConsensusPathDB, HPO, mouse homolog genes, zebrafish homolog genes, HPO, OMIM, Orphanet have been updated.
The egenetics and GNF/Atlas expression, gene interactions and SORVA statistic have been retired.
LRT, FATHMM, fathmm-MKL, fitCons, LINSIGHT, GenoCanyon, EVE, Siphy scores, allele frequencies from ESP, ExAC, UK10K, and GTEx, eQTLGen and Geuvadis eQTLs have been retired.