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.

These are updated files which include chromosome 22. In version 1 of the files, chromosome 22 did not exist. The ranges and interpretations of the scores are the same as in the first version of the files.