Variant Overview

This section is only available for variants.

Common Information

Field Name	Description
VCF Column	Required Value
Variant Type	Type of the variant: SNV, insertion, deletion, MNV
Chromosome	The reference sequence name. Values are #, or chr#, where # is 1 of the following: •The chromosome number, as in 1–22. •The name, as in X or Y; M or MT for mitochondrial.
Start	Start position.
Stop	Stop position.
Variant ID	Variant ID from Nirvana, based on the Broad variant ID scheme.
Ref Allele	The reference allele.
Alt Allele	The alternate allele.
Genes	Name of the gene if applicable. A comma-delimited list is used for multiple genes.
Exons	Exon number(s) and the total exons for the active transcript, as applicable. A comma-delimited list is used for multiple exons.
Cytogenetic Band	Cytoband of variant.
All Consequences	Sequence Ontology consequences to describe how each variant impacts a given transcript.

External Links

Field Name	Description
Database	Database Description
IGV	Integrative Genomics Viewer (IGV) is an open-source genome browser and visualization tool used to observe biologically interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from DNA microarrays.
LOVD	The Leiden Open Variation Database (LOVD) is an open-source database focused on the combination between a gene and a genetic (heritable) disease.
UCSC Browser	An interactive database offering access to genome sequence data from various vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.
Ensembl	A bioinformatics project organizing biological information around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of individual genomes, and of the synteny and orthology relationships between them..
gnomAD	A database that aggregates and harmonizes both exome and genome sequencing data from a wide variety of large-scale sequencing projects.
COSMIC	An online database of somatically acquired mutations found in human cancer. This link opens COSMIC in a new browser tab.
Google Scholar	Google Scholar provides a way to broadly search for scholarly literature. Search across many disciplines and sources, including: • Articles • Theses • Books • Abstracts This information comes from academic publishers, professional societies, online repositories, universities, and other web sites.
PubMed	PubMed allows you to search for literature for the variant.
LitVar	LitVar allows you to search for literature for the variant. This is available for any variant with an RSID.
Mastermind	Mastermind allows you to search for literature for the variant. This is available for any variant with an hgvsg annotation.