Resources and Tools

DECIPHER

DECIPHER (Database of genomic variation and phenotype in humans using Ensembl resources) is an interactive web-based database which incorporates a suite of tools designed to aid the interpretation of genomic variants. Version 11.0, a major new version, was released on December 9th 2020. This version visualises genomic data in GRCh38 and supports MANE transcripts. More information on the latest improvements can be found on the webpage.

gene2phenotype

The genotype-to-phenotype (G2P) database provides detailed information on which particular genotypes lead to which disease phenotypes. It is a publicly-accessible online system designed to facilitate the development, validation, curation and distribution of large-scale, evidence-based datasets for use in diagnostic variant filtering.

Gene Curation Coalition Database

The Gene Curation Coalition (GenCC) Database (DB) provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases. Curated gene-disease relationships are submitted by GenCC member organisations, comprising organisations that provide online resources, such as TGMI’s G2P, ClinGen, DECIPHER, Genomics England PanelApp, as well as diagnostic laboratories that have committed to sharing their internal curated gene-level knowledge. In December 2020, the GenCC DB was launched on the GenCC website.

The MANE project

The MANE (Matched Annotation from the NCBI and EMBL-EBI) project aims to simplify variant interpretation by defining a joint ‘default’ transcript set standardised across genomics browsers. On this page we share updates on the progress of this part of the TGMI.

Transcript Archive (Tark)

The goal of Tark is to create an archive of all transcript sequences from all sources, including historical gene sets. The beta site is made available to give the community the opportunity to explore Tark functionality.

VEP plugin – uORF variants

Variant Effect Predictor (VEP) plugin tool to annotate 5’UTR variants can be found here.