ArticleHuman mutation2018
hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update.
Article in Human mutation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed.
- Deep Learning Predicts Mutations and Outcomes in Gastrointestinal Stromal Tumors.Cancer research · 2026Article
- Convergence of machine learning and genomics for precision oncology.Nature reviews. Cancer · 2026Review
- Investigating the oncogenic role of aberrant EZH2 in hepatoblastoma.Scientific reports · 2026Article
- Prediction of Mutations and Outcome in Gastrointestinal Stromal Tumors with Deep Learning: A Multicenter, Multinational Study.medRxiv : the preprint server for health sciences · 2026Article
- VarSim: A Python Toolkit for HGVS Variant Description Validation, Normalization, and Representation Conversion.Human mutation · 2026Article
- Genetic data normalization for genomic medicine: a Fast Healthcare Interoperability Resources Genomics reference implementation.Journal of the American Medical Informatics Association : JAMIA · 2025Article
- MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays.Genome biology · 2025Article
- Standardizing variant naming in literature with VariantValidator to increase diagnostic rates.Nature genetics · 2024Article
- Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms.bioRxiv : the preprint server for biology · 2024Article
- Estimation of hereditary fructose intolerance prevalence in the Chinese population.Orphanet journal of rare diseases · 2022Review
- Clinical significance of genetic variation in hypertrophic cardiomyopathy: comparison of computational tools to prioritize missense variants.Frontiers in cardiovascular medicine · 2022Article
- Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature.Briefings in bioinformatics · 2021Review
- Methods and feasibility study for exome sequencing as a universal second-tier test in newborn screening.Genetics in medicine : official journal of the American College of Medical Genetics · 2021Article
- Whole exome sequencing of a family revealed a novel variant in the CHM gene, c.22delG p.(Glu8Serfs*4), which co-segregated with choroideremia.Bioscience reports · 2020Article
- Application of targeted panel sequencing and whole exome sequencing for 76 Chinese families with retinitis pigmentosa.Molecular genetics & genomic medicine · 2020Article
- SPDI: data model for variants and applications at NCBI.Bioinformatics (Oxford, England) · 2020Article
- Article
- Variation in nomenclature of somatic variants for selection of oncological therapies: Can we reach a consensus soon?Human mutation · 2020Article
- hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update.Human mutation · 2018Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
The Human Genome Variation Society (HGVS) nomenclature guidelines encourage the accurate and standard description of DNA, RNA, and protein sequence variants in public variant databases and the scientific literature. Inconsistent application of the HGVS guidelines can lead to misinterpretation of variants in clinical settings. Reliable software tools are essential to ensure consistent application of the HGVS guidelines when reporting and interpreting variants. We present the hgvs Python package, a comprehensive tool for manipulating sequence variants according to the HGVS nomenclature guidelines. Distinguishing features of the hgvs package include: (1) parsing, formatting, validating, and normalizing variants on genome, transcript, and protein sequences; (2) projecting variants between aligned sequences, including those with gapped alignments; (3) flexible installation using remote or local data (fully local installations eliminate network dependencies); (4) extensive automated tests; and (5) open source development by a community from eight organizations worldwide. This report summarizes recent and significant updates to the hgvs package since its original release in 2014, and presents results of extensive validation using clinical relevant variants from ClinVar and HGMD.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.