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.
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.