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Fig. 3 | BMC Medical Genomics

Fig. 3

From: Genome analysis and knowledge-driven variant interpretation with TGex

Fig. 3

Variant analysis and interpretation. This figure shows several views in TGex providing detailed information and useful links to source data, with the goal to improve and hasten expert variant interpretation. a VarElect MiniCards. The extensive gene-phenotype hit-context evidence from the GeneCards knowledgebase is portrayed in the MiniCards. This figure shows selected parts of the MiniCard for the gene TTC37 and the phenotypes used in the congenital diarrhea case. A list of matched phenotypes is shown in red in the top part, followed by extensive gene-centric evidence for queried phenotype association from various GeneCards sections. This is combined with MalaCards-based evidence, similarly showing queried phenotype associations in diseases associated with the gene TTC37, from various MalaCards sections. Search terms are highlighted throughout the text, and links to specific GeneCards/MalaCards webcard positions enable further scrutiny via more detailed evidence exploration within the knowledgebase. b Variant and evidence selection. Several types of marks can be defined per candidate variant by the analyst, upon clicking the ‘Annotate variant’ button located to the left of each variant row. This includes relevance (High, Med or Low), the pathogenicity of the variant, and a free text note. Below, information pieces regarding the variant/gene pathogenicity can be selected, based on VarElect MiniCards and OMIM disease records. The selected variants and their annotations are propagated to the report. c Gene view. A gene-centric summary for the gene TTC37, including associated diseases, mode of inheritance, and pathogenic variants summary, based on OMIM and ClinVar records. d ClinVar information – ClinVar records matching a given variant, including the condition and clinical significance. e ACMG score – Clinical significance based on the ACMG score. Clicking upon the variant clinical significance value shows a detailed view of the data used for the classification.

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