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.本文件包含关联研究论文中所述的AlphScore_final数据集。该数据集基于dbNSFP 4.2a构建，包含表头，采用制表符分隔格式，并通过bgzip进行压缩。各列内容如下：#chr：染色体（hg38）；pos(1-based)：位置（hg38，1-based坐标）；ref：参考等位基因；alt：替代等位基因；aaref：参考氨基酸；aaalt：替代氨基酸；rs_dbSNP：dbSNP数据库的rs编号；hg19_chr：染色体（hg19）；hg19_pos(1-based)：位置（hg19，1-based坐标）；ID：变异ID，格式为：染色体:位置:参考氨基酸:替代氨基酸；genename：基因名称，取自dbNSFP；Uniprot_acc_split：用于构建AlphScore_final的结构模型的UniProt ID（多个条目以分号分隔）；Uniprot_acc：dbNSFP提供的UniProt ID；HGVSp_VEP_split：用于构建AlphScore_final的错义变异，这些变异与Uniprot_acc_split对应的条目相匹配；HGVSp_VEP：dbNSFP提供的HGVSp_VEP格式变异注释；CADD_raw：dbNSFP提供的CADD_raw分值；REVEL_score：dbNSFP提供的REVEL_score分值；DEOGEN2_score：dbNSFP提供的DEOGEN2_score分值；b_factor：对应残基的AlphaFold pLDDT评分（若某变异影响多个蛋白质，则按Uniprot_acc_split中指定的蛋白质顺序以分号分隔给出对应评分）；SOLVENT_ACCESSIBILITY_core：通过DSSP计算得到的残基Cα原子溶剂可及性（若某变异影响多个蛋白质，则按Uniprot_acc_split中指定的蛋白质顺序以分号分隔给出对应数值）；in_gnomad_train：若该变异位于用于训练的gnomAD数据集内，则取值为TRUE；in_clinvar_ds：若该变异位于用于联合评分模型验证/训练的ClinVar数据集内，则取值为TRUE；AlphScore：本列对应AlphScore_final；glm_AlphCadd：本列对应AlphScore_final与CADD的组合评分；glm_AlphRevel：本列对应AlphScore_final与REVEL的组合评分；glm_RevelCadd：本列对应REVEL与CADD的组合评分；glm_AlphRevelCadd：本列对应AlphScore_final、REVEL与CADD的组合评分；glm_AlphDeogen：本列对应AlphScore_final与DEOGEN2的组合评分；glm_CaddDeogen：本列对应CADD与DEOGEN2的组合评分；glm_DeogenRevel：本列对应DEOGEN2与REVEL的组合评分；glm_AlphDeogenRevel：本列对应AlphScore_final、DEOGEN2与REVEL的组合评分；glm_AlphCaddDeogen：本列对应AlphScore_final、CADD与DEOGEN2的组合评分；glm_CaddDeogenRevel：本列对应CADD、DEOGEN2与REVEL的组合评分。请注意，知识共享（Creative Commons）许可仅适用于AlphScore_final的数值。REVEL、CADD评分以及包含REVEL与CADD的组合评分不可用于商业用途。完整的参考文献列表可参见我们的研究手稿。