gnomAD annotated search

We've introduced an exciting new way to browse and filter variants using annotations provided by gnomAD for exomes. The existing search, which is based on the pipeline provided annotations, is unchanged and can still be used in the usual way. This format of the search looks at the same data, but viewed in a different way. There are several differences between 2 search mechanisms. The primary difference is that the pipeline annotated search is never updated and represents the annotations that were current at the time they were analyzed. On the other hand, the gnomAD annotated search is updated quarterly with every new release of gnomAD across all previously analyzed patients. By using the latest frequencies and gene names, we can go back and review cases that were previously unsolved. There are several other differences that should be noted: The pipeline annotated search displays ONE variant linked to ONE transcript. With the gnomAD annotated search, we are displaying transcripts (not variants), which means for one variant we can have MULTIPLE transcripts. The significance of this is that in the search results, we may see multiple rows for the same variant, represented by different transcripts. The other difference, are the tabbed search results. The pipeline annotated search currently shows a single tab for all search results. With gnomAD annotated search, we are splitting the results into 2 tabs. The first tab displays variants that have a link to a gnomAD record. The second tabs lists variants that have no link to gnomAD. By default, the gnomAD annotated search assumes the assembly build is GRCh38. If users need to go back and look at previously analyzed patients, they should remember to switch the assembly to GRCh37. Some new filters were introduced including: LoF (loss of function), Homozygous count, Canonical, and gnomAD consequence. It should be noted that structural variants are not supported in the gnomAD annotated search. To search SVs, please continue to use the pipeline annotated search. The new gnomAD search is not meant to replace the pipeline search, but to complement it with fresh new information for the variants gnomAD has coverage for which has far lower coverage than the pipeline. It is highly recommended to use both. For a demonstration video please follow this link: https://youtu.be/iGRiP8hmet8

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