{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,5]],"date-time":"2026-03-05T06:58:18Z","timestamp":1772693898054,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2020,12,1]],"date-time":"2020-12-01T00:00:00Z","timestamp":1606780800000},"content-version":"vor","delay-in-days":335,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Dean\u2019s Bequest Fund"},{"name":"New Zealand Tertiary Education Commission Centre of Research Excellence (CoRE) grant to the Bio-Protection Research Centre"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Variants within the non-coding genome are frequently associated with phenotypes in genome-wide association studies. These non-coding regions may be involved in the regulation of gene expression, encode functional non-coding RNAs, or influence splicing and other cellular functions. We have curated a list of characterized non-coding human genome variants based on the published evidence that indicates phenotypic consequences of the variation. In order to minimize annotation errors, two curators have independently verified the supporting evidence for pathogenicity of each non-coding variant in the published literature. The database consists of 721 non-coding variants linked to the published literature describing the evidence of functional consequences. We have also sampled 7228 covariate-matched benign controls, that have a population frequency of over 5%, from the single nucleotide polymorphism database (dbSNP151) database. These were sampled controlling for potential confounding factors such as linkage with pathogenic variants, annotation type (untranslated region, intron, intergenic, etc.) and variant type (substitution or indel). The dataset presented here represents a curated repository, with a potential use for the training or evaluation of algorithms used in the prediction of non-coding variant functionality.<\/jats:p><jats:p>Database URL: https:\/\/github.com\/Gardner-BinfLab\/ncVarDB.<\/jats:p>","DOI":"10.1093\/database\/baaa105","type":"journal-article","created":{"date-parts":[[2020,11,13]],"date-time":"2020-11-13T04:20:07Z","timestamp":1605241207000},"source":"Crossref","is-referenced-by-count":15,"title":["ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls"],"prefix":"10.1093","volume":"2020","author":[{"given":"Harry","family":"Biggs","sequence":"first","affiliation":[{"name":"Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand"}]},{"given":"Padmini","family":"Parthasarathy","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1885-1108","authenticated-orcid":false,"given":"Alexandra","family":"Gavryushkina","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand"},{"name":"Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7808-1213","authenticated-orcid":false,"given":"Paul P","family":"Gardner","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand"},{"name":"Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand"}]}],"member":"286","published-online":{"date-parts":[[2020,12,1]]},"reference":[{"key":"2020120621230011200_R1","volume-title":"The Database of Short Genetic Variation (dbSNP)","author":"Kitts","year":"2014"},{"key":"2020120621230011200_R2","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nature09534","article-title":"A map of human genome variation from population-scale sequencing","volume":"467","author":"1000 Genomes Project Consortium","year":"2010","journal-title":"Nature"},{"key":"2020120621230011200_R3","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nature15394","article-title":"An integrated map of structural variation in 2,504 human genomes","volume":"526","author":"Sudmant","year":"2015","journal-title":"Nature"},{"key":"2020120621230011200_R4","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/j.ajhg.2017.06.005","article-title":"10 years of GWAS discovery: biology, function, and translation","volume":"101","author":"Visscher","year":"2017","journal-title":"Am. 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