“TogoVar”https://togovar.org/, a comprehensive Japanese genetic variation database, is continuously adding new functions and expanding data. We are pleased to announce the data update as follows

• MGeND (Medical Genomics Japan Variant Database), which contains genomic variants with clinical characteristics collected through the Integrated Clinical Genomic Information Database Project conducted by AMED (Japan Agency for Medical Research and Development), has been added. MGeND includes variant information related to cancer, rare and intractable diseases, infectious diseases, dementia, and hearing loss, and is considered the Japanese equivalent of ClinVar.

• JGA-WGS dataset, which aggregates allele frequencies and genotype counts by reanalyzing whole-genome sequence data deposited in NBDC Human Database / Japanese Genotype-phenotype Archive (JGA), has also been added. The reference genome is GRCh38. For details on the reanalysis, refer to the “Whole genome sequencing analysis data (germline)” on NBDC Human Database website.

• Missense variants are visualized on a 3D protein structure. The visualization helps you assess the potential impact of each missense variant on a protein structure (e.g., BRAF:p.V600E, KRAS:p.G12D). You can choose from protein structures registered in Protein Data Bank Japan (PDBj) or those predicted by AlphaFold. Please note that the displayed structures do not account for the effects of the variant.