Published February 25, 2022
| Version v1
Dataset
Open
AlphScore_final dataset
Authors/Creators
- 1. Institute of Human Genetics, University Bonn, and School of Medicine, University Hospital Bonn, Germany
- 2. Berlin Institute of Health at Charité – Universitätsmedizin Berlin , Berlin, Germany
- 3. Institute for Genomic Statistics and Bioinformatics, University Hospital of Bonn, University of Bonn, Bonn, Germany; Institute of Medical Biometry, Informatics and Epidemiology, University Hospital of Bonn, University of Bonn, Bonn, Germany
- 4. Berlin Institute of Health at Charité – Universitätsmedizin Berlin , Berlin, Germany; Institut für Humangenetik, Universität zu Lübeck, Lübeck, Germany
Description
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.