ArticleGenome medicine2017
ClinGen Pathogenicity Calculator: a configurable system for assessing pathogenicity of genetic variants.
Article in Genome medicine, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.
What it found
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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
37 citing papers in PubMed, 1 synthesis or guideline pooled it, 67 citations in OpenAlex.
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- CADD-ThresholdApp: an interactive web application for calibrating CADD scores using ClinVar.BMC bioinformatics · 2026Article
- ClinGen API platform for classification of human genetic variants.Cell genomics · 2026Article
- Incidence of non-colorectal/endometrial malignancies in individuals with Lynch syndrome: a retrospective cohort study.EClinicalMedicine · 2025Article
- Integrated data-driven biotechnology research environments.Database : the journal of biological databases and curation · 2025Review
- Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review.NPJ genomic medicine · 2024Review
- In-Depth Genomic Analysis: The New Challenge in Congenital Heart Disease.International journal of molecular sciences · 2024Review
- Prevalence of the cancer-associated germline variants in Russian adults and long-living individuals: using the ACMG recommendations and computational interpreters for pathogenicity assessment.Frontiers in oncology · 2024Article
- Variant curation and interpretation in hereditary cancer genes: An institutional experience in Latin America.Molecular genetics & genomic medicine · 2023Article
- vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines.Bioinformatics (Oxford, England) · 2023Article
- The global carrier frequency and genetic prevalence of Upshaw-Schulman syndrome.BMC genomic data · 2021Article
- Genotypes of European and Iranian patients with type 3 von Willebrand disease enrolled in 3WINTERS-IPS.Blood advances · 2021Article
- Challenges and opportunities for integrating genetic testing into a diagnostic workflow: heritable long QT syndrome as a model.Diagnosis (Berlin, Germany) · 2021Review
- Changes in genetic variant results over time in pediatric cardiomyopathy and electrophysiology.Journal of genetic counseling · 2021Article
- UniProt: the universal protein knowledgebase in 2021.Nucleic acids research · 2021Article
- EMQN best practice guidelines for molecular genetic testing and reporting of 21-hydroxylase deficiency.European journal of human genetics : EJHG · 2020Article
- Current challenges and possible future developments in personalized psychiatry with an emphasis on psychotic disorders.Heliyon · 2020Review
- Missense PALB2 germline variant disrupts nuclear localization of PALB2 in a patient with breast cancer.Familial cancer · 2020Article
- Practical Aspects in Genetic Testing for Cardiomyopathies and Channelopathies.The Clinical biochemist. Reviews · 2019Review
- Toward automation of germline variant curation in clinical cancer genetics.Genetics in medicine : official journal of the American College of Medical Genetics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
22 authors at 6 institutions in 1 country.
Funding
Abstract
backgroundThe success of the clinical use of sequencing based tests (from single gene to genomes) depends on the accuracy and consistency of variant interpretation. Aiming to improve the interpretation process through practice guidelines, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) have published standards and guidelines for the interpretation of sequence variants. However, manual application of the guidelines is tedious and prone to human error. Web-based tools and software systems may not only address this problem but also document reasoning and supporting evidence, thus enabling transparency of evidence-based reasoning and resolution of discordant interpretations.
resultsIn this report, we describe the design, implementation, and initial testing of the Clinical Genome Resource (ClinGen) Pathogenicity Calculator, a configurable system and web service for the assessment of pathogenicity of Mendelian germline sequence variants. The system allows users to enter the applicable ACMG/AMP-style evidence tags for a specific allele with links to supporting data for each tag and generate guideline-based pathogenicity assessment for the allele. Through automation and comprehensive documentation of evidence codes, the system facilitates more accurate application of the ACMG/AMP guidelines, improves standardization in variant classification, and facilitates collaborative resolution of discordances. The rules of reasoning are configurable with gene-specific or disease-specific guideline variations (e.g. cardiomyopathy-specific frequency thresholds and functional assays). The software is modular, equipped with robust application program interfaces (APIs), and available under a free open source license and as a cloud-hosted web service, thus facilitating both stand-alone use and integration with existing variant curation and interpretation systems. The Pathogenicity Calculator is accessible at http://calculator.clinicalgenome.org .
conclusionsBy enabling evidence-based reasoning about the pathogenicity of genetic variants and by documenting supporting evidence, the Calculator contributes toward the creation of a knowledge commons and more accurate interpretation of sequence variants in research and clinical care.
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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.