{"doi":"10.1038/s41586-022-04558-8","title":"A joint NCBI and EMBL-EBI transcript set for clinical genomics and research","abstract":"<jats:title>Abstract</jats:title><jats:p>Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, the absence of a standard for clinical reporting and browser display complicates the process of consistent interpretation and reporting. To address these challenges, Ensembl/GENCODE<jats:sup>1</jats:sup>and RefSeq<jats:sup>2</jats:sup>launched a joint initiative, the Matched Annotation from NCBI and EMBL-EBI (MANE) collaboration, to converge on human gene and transcript annotation and to jointly define a high-value set of transcripts and corresponding proteins. Here, we describe the MANE transcript sets for use as universal standards for variant reporting and browser display. The MANE Select set identifies a representative transcript for each human protein-coding gene, whereas the MANE Plus Clinical set provides additional transcripts at loci where the Select transcripts alone are not sufficient to report all currently known clinical variants. Each MANE transcript represents an exact match between the exonic sequences of an Ensembl/GENCODE transcript and its counterpart in RefSeq such that the identifiers can be used synonymously. We have now released MANE Select transcripts for 97% of human protein-coding genes, including all American College of Medical Genetics and Genomics Secondary Findings list v3.0 (ref.<jats:sup>3</jats:sup>) genes. MANE transcripts are accessible from major genome browsers and key resources. Widespread adoption of these transcript sets will increase the consistency of reporting, facilitate the exchange of data regardless of the annotation source and help to streamline clinical interpretation.</jats:p>","journal":"Nature","year":2022,"id":30938,"datarank":9.419745905242115,"base_score":6.371611847231857,"endowment":6.371611847231857,"self_citation_contribution":0.9557417770847787,"citation_network_contribution":8.464004128157336,"self_endowment_contribution":0.9557417770847787,"citer_contribution":8.464004128157336,"corpus_percentile":78.8,"corpus_rank":295,"citation_count":584,"citer_count":200,"citers_with_citation_signal":200,"citers_with_endowment":200,"datacite_reuse_total":25,"is_dataset":true,"is_dataset_confidence":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":166943,"name":"Shashikant Pujar","orcid":null,"position":1,"is_corresponding":false},{"id":24498,"name":"Jane E. Loveland","orcid":null,"position":2,"is_corresponding":false},{"id":166944,"name":"Alex Astashyn","orcid":null,"position":3,"is_corresponding":false},{"id":42924,"name":"Ruth Bennett","orcid":"0000-0002-9009-4607","position":4,"is_corresponding":false},{"id":42926,"name":"Andrew Berry","orcid":"0000-0001-5096-7701","position":5,"is_corresponding":false},{"id":166945,"name":"Eric Cox","orcid":"0000-0001-7691-4835","position":6,"is_corresponding":false},{"id":105333,"name":"Claire Davidson","orcid":"0000-0002-4910-8202","position":7,"is_corresponding":false},{"id":166946,"name":"Olga Ermolaeva","orcid":null,"position":8,"is_corresponding":false},{"id":81090,"name":"Catherine M. Farrell","orcid":"0009-0003-3804-8528","position":9,"is_corresponding":false},{"id":105336,"name":"Reham Fatima","orcid":"0000-0002-9914-4893","position":10,"is_corresponding":false},{"id":61879,"name":"Laurent Gil","orcid":"0000-0002-9475-4502","position":11,"is_corresponding":false},{"id":166947,"name":"Tamara Goldfarb","orcid":null,"position":12,"is_corresponding":false},{"id":37971,"name":"Jose Manuel Gonzalez","orcid":"0000-0001-5569-0705","position":13,"is_corresponding":false},{"id":51337,"name":"Diana Haddad","orcid":null,"position":14,"is_corresponding":false},{"id":43255,"name":"Matthew P. Hardy","orcid":"0000-0001-6420-1715","position":15,"is_corresponding":false},{"id":18874,"name":"Toby Hunt","orcid":"0000-0001-8377-0841","position":16,"is_corresponding":false},{"id":166948,"name":"John Jackson","orcid":null,"position":17,"is_corresponding":false},{"id":166949,"name":"Vinita S. Joardar","orcid":null,"position":18,"is_corresponding":false},{"id":43042,"name":"Michael Kay","orcid":null,"position":19,"is_corresponding":false},{"id":166950,"name":"Vamsi K. Kodali","orcid":null,"position":20,"is_corresponding":false},{"id":166951,"name":"Kelly M. McGarvey","orcid":null,"position":21,"is_corresponding":false},{"id":88400,"name":"Aoife McMahon","orcid":"0000-0003-0978-0309","position":22,"is_corresponding":false},{"id":105367,"name":"Jonathan M. Mudge","orcid":"0000-0003-4789-7495","position":23,"is_corresponding":false},{"id":124695,"name":"Daniel N. Murphy","orcid":null,"position":24,"is_corresponding":false},{"id":75506,"name":"Michael R. Murphy","orcid":"0000-0002-0470-5791","position":25,"is_corresponding":false},{"id":81103,"name":"Bhanu Rajput","orcid":null,"position":26,"is_corresponding":false},{"id":166952,"name":"Sanjida H. Rangwala","orcid":null,"position":27,"is_corresponding":false},{"id":81104,"name":"Lillian D. Riddick","orcid":null,"position":28,"is_corresponding":false},{"id":2130,"name":"Françoise Thibaud‐Nissen","orcid":"0000-0003-4957-7807","position":29,"is_corresponding":false},{"id":2114,"name":"Glen Threadgold","orcid":"0000-0002-4475-0183","position":30,"is_corresponding":false},{"id":166953,"name":"Anjana R. Vatsan","orcid":null,"position":31,"is_corresponding":false},{"id":81088,"name":"Craig Wallin","orcid":null,"position":32,"is_corresponding":false},{"id":81105,"name":"David Webb","orcid":"0000-0003-4243-4002","position":33,"is_corresponding":false},{"id":105371,"name":"Paul Flicek","orcid":"0000-0002-3897-7955","position":34,"is_corresponding":false},{"id":117922,"name":"Ewan Birney","orcid":"0000-0001-8314-8497","position":35,"is_corresponding":false},{"id":2100,"name":"Kim D. Pruitt","orcid":"0000-0001-7950-1374","position":36,"is_corresponding":false},{"id":105364,"name":"Adam Frankish","orcid":"0000-0002-4333-628X","position":37,"is_corresponding":false},{"id":35062,"name":" Fiona Cunningham","orcid":"0000-0002-7445-2419","position":38,"is_corresponding":false},{"id":2099,"name":"Terence D. Murphy","orcid":"0000-0001-9311-9745","position":39,"is_corresponding":false},{"id":88401,"name":"Joannella Morales","orcid":"0000-0002-8121-9797","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":6.371611847231857,"endowment":6.371611847231857,"datacite_reuse_total":25,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"35388217","pmcid":"PMC9007741","openalex_id":"https://openalex.org/W4224014283","authors":[],"funders":[{"funder_name":"Wellcome Trust","grant_id":"WT200990/A/16/Z","title":null},{"funder_name":"NHGRI NIH HHS","grant_id":"U24 HG007234","title":null},{"funder_name":"Medical Research Council","grant_id":"MC_PC_19024","title":null},{"funder_name":"Wellcome Trust","grant_id":"WT108749/Z/15/Z","title":null},{"funder_name":"NHGRI NIH HHS","grant_id":"U41 HG007234","title":null},{"funder_name":"Wellcome Trust","grant_id":"WT200990/Z/16/Z","title":null},{"funder_name":"Wellcome Trust","grant_id":"200990","title":"Designing, developing and delivering integrated foundations for genomic medicine"},{"funder_name":"National Institutes of Health","grant_id":"5U41HG007234-08","title":"GENCODE: comprehensive genome annotation for human and mouse"},{"funder_name":"Wellcome Trust","grant_id":"108749","title":"ENSEMBL"},{"funder_name":"Wellcome Trust","grant_id":"","title":null},{"funder_name":"Wellcome Trust","grant_id":"","title":null}],"total_grants":11,"fwci":98.6294,"citation_percentile":0.99979233,"influential_citations":41,"citation_trend":[{"year":2022,"count":46},{"year":2023,"count":102},{"year":2024,"count":179},{"year":2025,"count":184},{"year":2026,"count":73}],"oa_status":"hybrid","license":"cc-by","oa_locations":[{"url":"https://www.nature.com/articles/s41586-022-04558-8.pdf","host_type":"journal"},{"url":"https://www.nature.com/articles/s41586-022-04558-8.pdf","host_type":"HYBRID"},{"url":"https://www.nature.com/articles/s41586-022-04558-8.pdf","host_type":"publisher"},{"url":"https://www.nature.com/articles/s41586-022-04558-8","host_type":"publisher"},{"url":"https://doi.org/10.1038/s41586-022-04558-8","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/35388217","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9007741","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC9007741","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC9007741?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1038/s41586-022-04558-8","host_type":""},{"url":"https://doi.org/https://doi.org/10.1038/s41586-022-04558-8","host_type":""}],"fields_of_study":["Genomics and Rare Diseases","Genomics and Phylogenetic Studies","Genomic variations and chromosomal abnormalities","Medicine","Biology","Computer Science","0301 basic medicine","0303 health sciences","03 medical and health sciences","Computational Biology","Databases, Genetic","Genome","Genomics","Humans","Information Dissemination","Molecular Sequence Annotation","National Library of Medicine (U.S.)","United States"],"mesh_terms":["Humans","National Library of Medicine (U.S.)","United States","Genome","Computational Biology","Genomics","Databases, Genetic","Information Dissemination","Molecular Sequence Annotation"],"keywords":["Ensembl","RefSeq","Annotation","Genome browser","Gene Annotation","Computational biology","Gene nomenclature","Genome project","Gene","Genome","Human genome","Genomics","Genetics","Biology","Bioinformatics","National Library of Medicine (U.S.)","Information Dissemination","610","Molecular Sequence Annotation","United States","576","Databases, Genetic","Humans","Analysis"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Partnerships for the goals"}],"linked_datasets":[{"doi":"10.6084/m9.figshare.26686002.v1","title":"Additional file 3 of Combining full-length gene assay and SpliceAI to interpret the splicing impact of all possible SPINK1 coding variants","publisher":"figshare","resource_type":"Presentation"},{"doi":"10.6084/m9.figshare.26686002","title":"Additional file 3 of Combining full-length gene assay and SpliceAI to interpret the splicing impact of all possible SPINK1 coding variants","publisher":"figshare","resource_type":"Presentation"},{"doi":"10.6084/m9.figshare.26685999.v1","title":"Additional file 2 of Combining full-length gene assay and SpliceAI to interpret the splicing impact of all possible SPINK1 coding variants","publisher":"figshare","resource_type":"Presentation"},{"doi":"10.6084/m9.figshare.26685999","title":"Additional file 2 of Combining full-length gene assay and SpliceAI to interpret the splicing impact of all possible SPINK1 coding variants","publisher":"figshare","resource_type":"Presentation"},{"doi":"10.6084/m9.figshare.23691127.v1","title":"Additional file 1 of A computational analysis reveals eight novel high-risk single nucleotide variants of human tumor suppressor LHPP gene","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.23691127","title":"Additional file 1 of A computational analysis reveals eight novel high-risk single nucleotide variants of human tumor suppressor LHPP gene","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.24465127.v1","title":"Additional file 1 of CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.24465127","title":"Additional file 1 of CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.24465317.v1","title":"Additional file 2 of CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.24465317","title":"Additional file 2 of CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.25107728.v1","title":"Additional file 1 of Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.25107728","title":"Additional file 1 of Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.25720279.v1","title":"Additional file 2 of Differences in 5'untranslated regions highlight the importance of translational regulation of dosage sensitive genes","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.25720279","title":"Additional file 2 of Differences in 5'untranslated regions highlight the importance of translational regulation of dosage sensitive genes","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.26567603.v1","title":"Additional file 1 of SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.26567603","title":"Additional file 1 of SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.26634012.v1","title":"Additional file 4 of CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.26634012","title":"Additional file 4 of CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.26713891.v1","title":"Additional file 3 of Differences in 5'untranslated regions highlight the importance of translational regulation of dosage sensitive genes","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.26713891","title":"Additional file 3 of Differences in 5'untranslated regions highlight the importance of translational regulation of dosage sensitive genes","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.27042503.v1","title":"Additional file 1 of Splam: a deep-learning-based splice site predictor that improves spliced alignments","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.27042503","title":"Additional file 1 of Splam: a deep-learning-based splice site predictor that improves spliced alignments","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.27042506.v1","title":"Additional file 2 of Splam: a deep-learning-based splice site predictor that improves spliced alignments","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.27042506","title":"Additional file 2 of Splam: a deep-learning-based splice site predictor that improves spliced alignments","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.25720156","title":"Additional file 1 of Differences in 5'untranslated regions highlight the importance of translational regulation of dosage sensitive genes","publisher":"figshare","resource_type":"Dataset"}],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"bioproject"},{"name":"ensembl"},{"name":"hgnc"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-09T05:58:09.560469Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}