AlphScore_final dataset

This file contains AlphScore_final as described in our associated publication. The file is based on dbNSFP 4.2a, contains a header and is tab-separated and compressed using bgzip. The columns contain the following content: #chr chromosome (hg38) pos(1-based) position (hg38) ref reference allele alt alternative allele aaref reference amino acid aaalt alternative amino acid rs_dbSNP rs number hg19_chr chromosome (hg19) hg19_pos(1-based) position (hg19) ID variant id in the format: chromosome:position:reference amino acid:alternative amino acid genename genename, taken from dbNSFP Uniprot_acc_split The Uniprot-IDs of the structural models that were used to create AlphScore_final (multiple entries separated by ; ) Uniprot_acc Uniprot_acc as provided by dbNSFP HGVSp_VEP_split The missense variant(s) as used to create AlphScore_final; these variant(s) correspond(s) to the Uniprot_acc_split HGVSp_VEP HGVSp_VEP as provided by dbNSFP CADD_raw CADD_raw as provided by dbNSFP REVEL_score REVEL_score as provided by dbNSFP DEOGEN2_score DEOGEN2_score as provided by dbNSFP b_factor AlphaFold's pLDDT-score of the residue (if a variant affects multiple proteins, the values of the proteins as indicated in Uniprot_acc_split are given separated by ; ). SOLVENT_ACCESSIBILITY_core Solvent accessibility of the residue as calculated for C-alpha by DSSP (if a variant affects multiple proteins, the values of the proteins as indicated in Uniprot_acc_split are given separated by ; ). in_gnomad_train TRUE if the variant was in the gnomAD set used for training in_clinvar_ds TRUE if the variant was in the ClinVar set used for validation / training of combined scores AlphScore This column corresponds to AlphScore_final glm_AlphCadd This column corresponds to AlphScore_final + CADD glm_AlphRevel This column corresponds to AlphScore_final + REVEL glm_RevelCadd This column corresponds to REVEL + CADD glm_AlphRevelCadd This column corresponds to AlphScore_final + REVEL + CADD glm_AlphDeogen This column corresponds to AlphScore_final + DEOGEN2 glm_CaddDeogen This column corresponds to CADD + DEOGEN2 glm_DeogenRevel This column corresponds to DEOGEN2 + REVEL glm_AlphDeogenRevel This column corresponds to AlphScore_final + DEOGEN2 + REVEL glm_AlphCaddDeogen This column corresponds to AlphScore_final + CADD + DEOGEN2 glm_CaddDeogenRevel This column corresponds to CADD + DEOGEN2 + REVEL Note that the Creative Commons license applies only to the values of AlphScore_final. REVEL and CADD scores as well as combined scores containing REVEL and CADD are not licensed for commercial use. The full list of references can be found in our manuscript.