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Variation Reporter specifications

Information


Unique identifier OMICS_03770
Name Variation Reporter
Interface Web user interface
Restrictions to use None
Input data Variation Reporter accepts input data in the form of variant definitions to query our databases.
Output data The report we generate includes molecular consequences, 1000Genome minor allele frequencies (MAF), clinical significance and citations. For novel variants (those not in our archive), we compute molecular consequences based on RefSeq transcripts.
Computer skills Basic
Stability Stable
Maintained Yes

Variation Reporter citations

 (3)
library_books

A variant by any name: quantifying annotation discordance across tools and clinical databases

2017
Genome Med
PMCID: 5267466
PMID: 28122645
DOI: 10.1186/s13073-016-0396-7

[…] rces are updating and improving, any tool or database used for clinical diagnostic purposes should be evaluated with rigorous scrutiny. Our results show that there are resources, including COSMIC and Variation Reporter, that claim to provide HGVS nomenclature when it is clear that they do not always comport with recommended conventions. As these standards are continuously being updated, resources […]

library_books

Human Chromosome Y and Haplogroups; introducing YDHS Database

2015
PMCID: 4477006
PMID: 26061870
DOI: 10.1186/s40169-015-0060-7

[…] for predicting mutations affecting protein function, but additional tools to increase the prediction accuracy for rare polymorphisms were considered important. PROVEAN (http://provean.jcvi.org/) and Variation Reporter (http://www.ncbi.nlm.nih.gov/variation/tools/reporter) from NCBIs ClinVar toolkit were added to increase the prediction capabilities of YDHS. These tools used in sync can provide va […]

library_books

Genomic convergence and network analysis approach to identify candidate genes in Alzheimer's disease

2014
BMC Genomics
PMCID: 4028079
PMID: 24628925
DOI: 10.1186/1471-2164-15-199

[…] anderer web server [].Further, for the GWA dataset, 19,532 single nucleotide polymorphisms (SNPs) with p value <0.0001 [] were selected. These SNPs were mapped to their corresponding genes using NCBI Variation Reporter, SCAN (SNP and CNV Annotation) database [] and SPOT web tool []. This led us to the identification of 1,686 genes which were ranked based on weighted p value obtained though genomic […]

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