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.