TogoVar Downloadable data for GRCh38

Last Updated: 2024/12/3

## Molecular annotation plus ClinVar

### Key Identification Values

Each record is uniquely identified by the combination of tgv_id and transcript_id.

### Data Sources
- Columns from tgv_id to alphamissense_score were obtained from the TogoVar annotation dataset: https://grch38.togovar.org/downloads/release/20241203/grch38/annotation/
- Columns from CLINSIG to CLNSIGSCV were extracted from the ClinVar VCF file: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar_20250209.vcf.gz

### Description for Columns

Variable name                         Description
------------------------------------------------------------------------------------------------------------------------
tgv_id                                :Togovar ID
rs                                    :dbSNP rs number
chr                                   :chromosome number
position_grch38                       :chromosomal position on GRCh38
ref                                   :reference allele
alt                                   :alternate allele
symbol                                :HGNC gene symbol
transcript_id                         :Ensembl transcript ID
consequence                           :molecular consequence predicted by Variant Effect Predictor (VEP)
sift_qualitative_prediction           :qualitative prediction by SIFT
sift_score                            :SIFT score
polyphen2_qualitative_prediction      :qualitative prediction by PolyPhen2
polyphen2_score                       :PolyPhen2 score
alphamissense_pathogenicity           :variant classification by AlphaMissense: 'Likely pathogenic', 'Likely benign', 'ambiguous'. Details: https://asia.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#alphamissense
alphamissense_score                   :a continuous score between 0 and 1 predicted by AlphaMissense
CLNSIG                                :Aggregate germline classification for this single variant; multiple values are separated by a vertical bar
CLNDN                                 :ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB
CLNDISDB                              :Tag-value pairs of disease database name and identifier submitted for germline classifications, e.g. OMIM:NNNNNN
CLNREVSTAT                            :ClinVar review status of germline classification for the Variation ID
CLNSIGSCV                             :SCV accession numbers for the submissions that contribute to the aggregate germline classification in ClinVar; multiple values are separated by a vertical bar