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{"id":14156,"date":"2024-11-06T11:59:48","date_gmt":"2024-11-06T16:59:48","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=14156"},"modified":"2024-11-06T11:59:48","modified_gmt":"2024-11-06T16:59:48","slug":"improving-functional-data-clinvar","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/11\/06\/improving-functional-data-clinvar\/","title":{"rendered":"Update! Improving the Representation of Functional Data in ClinVar"},"content":{"rendered":"<h3><i><span data-contrast=\"auto\">We want your feedback!<\/span><\/i><span data-ccp-props=\"{}\">\u00a0<\/span><\/h3>\n<p><span data-contrast=\"auto\">As <\/span><a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/09\/10\/improving-representation-functional-data-clinvar\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=clinvar-functional-data-20241106\"><span data-contrast=\"none\">previously announced<\/span><\/a><span data-contrast=\"auto\">, NCBI is improving the way that functional data are submitted to <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/clinvar\/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=clinvar-functional-data-20241106\"><span data-contrast=\"none\">ClinVar<\/span><\/a><span data-contrast=\"auto\"> and how they are represented in the XML format and on the website. We have started enhancing support for functional data and would like your feedback!\u00a0<\/span><span data-ccp-props=\"{}\">\u00a0<\/span><\/p>\n<h5><b><span data-contrast=\"auto\">What\u2019s new?<\/span><\/b><span data-ccp-props=\"{}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"auto\">We have updated the GitHub repository with:<\/span><span data-ccp-props=\"{}\">\u00a0<\/span><\/p>\n<ul>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"3\" data-list-defn-props=\"{"335552541":1,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\"><a href=\"https:\/\/github.com\/ncbi\/clinvar\/tree\/master\/functional_data\/submission\">Updated submission templates<\/a>\u00a0\u00a0<\/span><\/li>\n<li data-leveltext=\"\uf0b7\" data-font=\"Symbol\" data-listid=\"3\" data-list-defn-props=\"{"335552541":1,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"\uf0b7","469777815":"hybridMultilevel"}\" aria-setsize=\"-1\" data-aria-posinset=\"1\" data-aria-level=\"1\"><span style=\"font-size: 17px;\"><a href=\"https:\/\/github.com\/ncbi\/clinvar\/tree\/master\/functional_data\/xsd\">Updated XSDs<\/a> and <a href=\"https:\/\/github.com\/ncbi\/clinvar\/tree\/master\/functional_data\/reporting\">sample XML files<\/a>\u00a0\u00a0<\/span><\/li>\n<\/ul>\n<p><!--more--><\/p>\n<p><b><span data-contrast=\"none\">Coming soon!<\/span><\/b><span data-contrast=\"none\"> Mock-ups for the VCV, or variant, web pages will be posted soon. <\/span><span data-contrast=\"auto\">Below is an illustration of how functional data could look in the new variant display.<\/span><span data-ccp-props=\"{"335557856":16777215,"335559739":0}\">\u00a0<\/span><\/p>\n<p><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"14158\" data-permalink=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/11\/06\/improving-functional-data-clinvar\/image-154\/\" data-orig-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/11\/image-154.png?fit=1621%2C477&ssl=1\" data-orig-size=\"1621,477\" data-comments-opened=\"1\" data-image-meta=\"{"aperture":"0","credit":"","camera":"","caption":"","created_timestamp":"0","copyright":"","focal_length":"0","iso":"0","shutter_speed":"0","title":"","orientation":"0"}\" data-image-title=\"image (154)\" data-image-description=\"\" data-image-caption=\"\" data-medium-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/11\/image-154.png?fit=300%2C88&ssl=1\" data-large-file=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/11\/image-154.png?fit=1024%2C301&ssl=1\" class=\"alignright size-full wp-image-14158\" src=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/11\/image-154.png?resize=1108%2C326&ssl=1\" alt=\"An illustration of how functional data could look in the new variant display. \" width=\"1108\" height=\"326\" srcset=\"https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/11\/image-154.png?w=1621&ssl=1 1621w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/11\/image-154.png?resize=300%2C88&ssl=1 300w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/11\/image-154.png?resize=1024%2C301&ssl=1 1024w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/11\/image-154.png?resize=150%2C44&ssl=1 150w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/11\/image-154.png?resize=768%2C226&ssl=1 768w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/11\/image-154.png?resize=1536%2C452&ssl=1 1536w, https:\/\/i0.wp.com\/ncbiinsights.ncbi.nlm.nih.gov\/wp-content\/uploads\/2024\/11\/image-154.png?resize=270%2C79&ssl=1 270w\" sizes=\"auto, (max-width: 1108px) 100vw, 1108px\" \/><\/p>\n<p><span data-contrast=\"none\">Functional data are a critical type of evidence for the classifications of both germline and somatic variants, particularly those with <\/span><span data-contrast=\"auto\">uncertain significance (VUS)<\/span><span data-contrast=\"none\">. For example, RNA-seq analysis may be performed to determine if variant at a splice junction affects splicing. Or an <\/span><i><span data-contrast=\"none\">in vitro <\/span><\/i><span data-contrast=\"none\">biochemical assay may be developed to measure the effect of every possible single nucleotide variant in a gene encoding an enzyme.<\/span><span data-ccp-props=\"{"335557856":16777215,"335559739":0}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"none\">Functional data may be submitted to ClinVar on its own or as part of the evidence for a classification. The ClinVar team will contact submitters who already have functional data in ClinVar to help them update and improve their contribution to ClinVar using the new format. Additionally, we anticipate allowing expert panels to provide assertions for the strength of functional evidence as annotations on submissions of functional data. These enhancements to ClinVar\u2019s data model and website will make it easier for clinical variant scientists and others to discover relevant functional data, whether generated as an experiment for a single variant or as a m<\/span><span data-contrast=\"auto\">ultiplex assay of variant effect (MAVE).\u00a0<\/span><span data-ccp-props=\"{"335557856":16777215,"335559739":0}\">\u00a0<\/span><\/p>\n<h5><b><span data-contrast=\"none\">Stay up to date\u202f<\/span><\/b><span data-ccp-props=\"{"335557856":16777215,"335559739":0}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"none\">Follow us on social\u202f<\/span><a href=\"https:\/\/www.linkedin.com\/company\/ncbinlm\"><span data-contrast=\"none\">@NCBI<\/span><\/a><span data-contrast=\"none\">\u202fand\u202f<\/span><a href=\"https:\/\/list.nih.gov\/cgi-bin\/wa.exe?SUBED1=CLINVAR&A=1\"><span data-contrast=\"none\">join our mailing list<\/span><\/a><span data-contrast=\"none\">\u202fto keep up to date on ClinVar.\u202f<\/span><span data-ccp-props=\"{"335557856":16777215,"335559739":0}\">\u00a0<\/span><\/p>\n<h5><b><span data-contrast=\"none\">We want to hear from you!<\/span><\/b><span data-ccp-props=\"{"335557856":16777215,"335559739":0}\">\u00a0<\/span><\/h5>\n<p><span data-contrast=\"auto\">We invite you to test your functional data in our new submission templates and to review the format for file download. Please provide your feedback to <\/span><a href=\"mailto:clinvar@ncbi.nlm.nih.gov\"><span data-contrast=\"none\">clinvar@ncbi.nlm.nih.gov<\/span><\/a><span data-contrast=\"auto\">.<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>We want your feedback!\u00a0 As previously announced, NCBI is improving the way that functional data are submitted to ClinVar and how they are represented in the XML format and on the website. We have started enhancing support for functional data and would like your feedback!\u00a0\u00a0 What\u2019s new?\u00a0 We have updated the GitHub repository with:\u00a0 Updated … <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2024\/11\/06\/improving-functional-data-clinvar\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Update! Improving the Representation of Functional Data in ClinVar<\/span> <span class=\"meta-nav\">→<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":14161,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_coblocks_attr":"","_coblocks_dimensions":"","_coblocks_responsive_height":"","_coblocks_accordion_ie_support":"","jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"Update! Improving the Representation of Functional Data in ClinVar","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false},"version":2}},"categories":[2248],"tags":[108204782],"table_tags":[],"class_list":["post-14156","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-clinvar"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Update! 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