ArticleDatabase : the journal of biological databases and curation2020
ncVarDB: a manually curated database for pathogenic non-coding variants and benign controls.
Article in Database : the journal of biological databases and curation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- AlphaGenome Atlas:medRxiv : the preprint server for health sciences · 2026Article
- A chromatin-structure-guided framework for predictive and interpretable regulatory genomics.Briefings in bioinformatics · 2026Article
- A Chromatin-Structure-Guided Framework for Predictive and Interpretable Regulatory Genomics.bioRxiv : the preprint server for biology · 2025Article
- Genome-wide functional annotation of variants: a systematic review of state-of-the-art tools, techniques and resources.Frontiers in pharmacology · 2025Review
- Language Modelling Techniques for Analysing the Impact of Human Genetic Variation.Bioinformatics and biology insights · 2025Review
- Regional-specific calibration enables application of computational evidence for clinical classification of 5' cis-regulatory variants in Mendelian disease.American journal of human genetics · 2024Article
- Multimodal learning of noncoding variant effects using genome sequence and chromatin structure.Bioinformatics (Oxford, England) · 2023Article
- Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications.Genome biology · 2023Article
- VariBench, new variation benchmark categories and data sets.Frontiers in bioinformatics · 2023Article
- Exploration of Tools for the Interpretation of Human Non-Coding Variants.International journal of molecular sciences · 2022Review
- The Current State of Genetic Testing Platforms for Inherited Retinal Diseases.Ophthalmology. Retina · 2022Article
- PhyloPGM: boosting regulatory function prediction accuracy using evolutionary information.Bioinformatics (Oxford, England) · 2022Article
- Insertions and deletions in the RNA sequence-structure map.Journal of the Royal Society, Interface · 2021Article
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Authors and funding
4 authors.
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Abstract
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. Database URL: https://github.com/Gardner-BinfLab/ncVarDB.
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