Create 2024-12-03-post2.md

_posts/en/2024-12-03-post2.md

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+---
+layout: post-en
+feed: false
+published: true
+tags:
+  - events
+  - public_relations
+category:
+ - en
+title: 'Data update for "TogoVar"'
+---
+“TogoVar”[https://togovar.org/](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)](https://mgend.ncgm.go.jp/), 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](https://mgend.ncgm.go.jp/) includes variant information related to cancer, rare and intractable diseases, infectious diseases, dementia, and hearing loss, and is considered the Japanese equivalent of [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/).
+
+- JGA-WGS dataset, which aggregates allele frequencies and genotype counts by reanalyzing whole-genome sequence data deposited in [NBDC Human Database](https://humandbs.dbcls.jp/en/) / [Japanese Genotype-phenotype Archive (JGA)](https://www.ddbj.nig.ac.jp/jga/index-e.html), has also been added. The reference genome is GRCh38. For details on the reanalysis, refer to the “[Whole genome sequencing analysis data (germline)](https://humandbs.dbcls.jp/en/data-processing)” 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](https://grch38.togovar.org/gene/1097#protein-structure), [KRAS:p.G12D](https://grch38.togovar.org/gene/6407#protein-structure)). You can choose from protein structures registered in [Protein Data Bank Japan (PDBj)](https://pdbj.org/?lang=en) or those predicted by [AlphaFold](https://alphafold.ebi.ac.uk/). Please note that the displayed structures do not account for the effects of the variant.