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h1: Beta version of the ClinGen Pathogenicity Calculator
p: Based on feedback from users and presentation to various groups, we have implemented several new features in this beta version of ClinGen Pathogenicity Calculator. We hope to deploy the calculator for users by the end of March 2016. We appreciate your time in trying out this beta version of calculator. We also look forward for more feedback, so we can continue improving the Calculator.
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h2: The dashboard (Entry Page) lists the alleles for which users have collected evidence.
p: Upon login user is able to see the list of alleles that he/she has created and input evidence of pathogenicity. This helps the user to quickly find out allele that he/she worked on. Also note the concise display of gene and allele visible on click.
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h2: Search Alleles in Registry using HGNC Gene Symbol
p: Entry page now provides search functionality to find alleles given HGNC approved gene symbol. The pagination at the bottom of the panel helps with quick navigation, especially when there are a large number of alleles are present for a given gene in the Registry. Searches based on gene are cached to make it faster, however, if you are searching a gene for first time, it might take a bit to return the results.
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h2: Link-outs to find more information about allele and/or gene if present
p: For preregistered alleles, the allele registry provides link-outs for to ExAC, dbSNP, Cosmic, ClinVar and myvariant.info. Also note the link-outs for gene for OMIM, NCBI, UCSC and HGNC.
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h2: Guide for evidence tags in every cell of evidence table.
p: It is difficult to memorize what each ACMG/AMP tag means. To help identify text associated with each ACMG tag, tag help is available. Other improvements in this panel include: 1) Users no longer need to enter the Tag-ID, and 2) Each tag can only be used once. The system will not accept an evidence tag twice. In addition to these improvements, the calculator interface includes a link to the ACMG Table for reference.
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h2: Download Evidence/Assertion report (Partially Implemented)
p: To have a copy of the evidence collected by users, generated reasoning, assertions and allele information, user can view the full view of document and print it (PDF/Printer) for reference.
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h2: Register new alleles (Coming Soon)!
p: It is likely that the variant that a user is interested in is not present in allele registry. In near future, users will be able to register a new allele from the calculator. If the HGVS based search does not return any hits, the calculator will prompt the user to register it. The HGVS expression will be validated on the fly, the allele normalized, and the transcript allele will be converted to a genomic allele and will become available for searching in the calculator.
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h2: Try the beta-version now!
p: The beta-version of the calculator is available for users to try. The calculator is deployed on our local server and is accessible through this Link. Mouse over <abbr title="betauser1">HERE</abbr> to see login and <abbr title="calculatorbetauser3316">HERE</abbr> to see password.
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