SynthesisHuman genetics2024
Variant effect predictors: a systematic review and practical guide.
Synthesis in Human genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A Framework for Bioinformatic Reporting in Prenatal Sequencing: Insights From a Systematic Review.Prenatal diagnosis · 2026Pooled it
- Assessment of the functionality and usability of open-source rare variant analysis pipelines.Briefings in bioinformatics · 2025Pooled it
- Functional effect predictions for ion channel missense variants using a protein language model.Journal of human genetics · 2026Article
- Genome-wide association study reveals loci associated with cytokine levels in chicken serum.Poultry science · 2026Article
- Association of IL-10 (rs1800896) and TLR3 (rs1879026) polymorphism with progression of hcv-related liver disease and hepatocellular carcinoma in Egyptian patients.BMC infectious diseases · 2026Article
- Advancing risk gene discovery across the allele frequency spectrum.HGG advances · 2026Review
- Assessing the Clinical Relevance ofCurrent oncology (Toronto, Ont.) · 2026Article
- Gene- and domain-aware calibration increases the clinical utility of variant effect predictors.Research square · 2026Article
- Benchmarking genetic birth prevalence estimates against newborn screening data.American journal of human genetics · 2026Article
- Feed-Forward Deep Neural Networks Predict Substrate-Specific Effects of Transporter Variants to Explain Drug Response Variability.Clinical and translational science · 2026Article
- Genetic background shapes AI-predicted variant effects.bioRxiv : the preprint server for biology · 2026Article
- Computational identification of rare pathogenic genomic variants in esophageal cancer markers: Transcript-level analysis, sequence-based insights, and structural-functional impacts of non-synonymous SNPs.Biochemistry and biophysics reports · 2026Article
- Application of qualifying variants for genomic analysis.Bioinformatics (Oxford, England) · 2026Article
- Predicting the functional impact of single nucleotide variants in Drosophila melanogaster with FlyCADD.Genetics · 2026Article
- Article
- Classification models distinguish functional and trafficking effects of KCNQ1 variants to enhance variant interpretation.bioRxiv : the preprint server for biology · 2025Article
- The first description of CTNNB1 syndrome in the Tunisian population: clinical investigation, molecular docking and molecular dynamics simulation of β-catenin/E-cadherin complex.Molecular biology reports · 2025Article
- Toward streamline variant classification: discrepancies in variant nomenclature and syntax for ClinVar pathogenic variants across annotation tools.Human genomics · 2025Article
- Language Modelling Techniques for Analysing the Impact of Human Genetic Variation.Bioinformatics and biology insights · 2025Review
- Predicting pathogen evolution and immune evasion in the age of artificial intelligence.Computational and structural biotechnology journal · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Large-scale association analyses using whole-genome sequence data have become feasible, but understanding the functional impacts of these associations remains challenging. Although many tools are available to predict the functional impacts of genetic variants, it is unclear which tool should be used in practice. This work provides a practical guide to assist in selecting appropriate tools for variant annotation. We conducted a MEDLINE search up to November 10, 2023, and included tools that are applicable to a broad range of phenotypes, can be used locally, and have been recently updated. Tools were categorized based on the types of variants they accept and the functional impacts they predict. Sequence Ontology terms were used for standardization. We identified 118 databases and software packages, encompassing 36 variant types and 161 functional impacts. Combining only three tools, namely SnpEff, FAVOR, and SparkINFERNO, allows predicting 99 (61%) distinct functional impacts. Thirty-seven tools predict 89 functional impacts that are not supported by any other tool, while 75 tools predict pathogenicity and can be used within the ACMG/AMP guidelines in a clinical context. We launched a website allowing researchers to select tools based on desired variants and impacts. In summary, more than 100 tools are already available to predict approximately 160 functional impacts. About 60% of the functional impacts can be predicted by the combination of three tools. Unexpectedly, recent tools do not predict more impacts than older ones. Future research should allow predicting the functionality of so far unsupported variant types, such as gene fusions.URL: https://cardio-care.shinyapps.io/VEP_Finder/ .Registration: OSF Registries on November 10, 2023, https://osf.io/s2gct .
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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.