Variant Overview

This section is only available for variants.

Common Information

Variant Type	Type of the variant (e.g., SNV, insertion, deletion, MNV, etc.)
Chromosome	Chromosome number, X, Y, or MT
Start	Start position.
Stop	Stop position.
Matched End Chromosome	Mate chromosome of a translocation.
Matched End Position	Mate position of a translocation.
Ref Allele	The reference allele.
Alt Allele	The alternate allele.
HGVSG	HGVSG nomenclature.
Selected Transcript HGVS	HGVSc and HGVSp (in both 3-letter and 1-letter form) change on the selected transcript.
ISCN	ISCN nomenclature.
Selected Transcript Exons	Exon impacted of the selected transcript.
Selected Transcript Consequences	Consequences of the variant on the selected transcript, in Sequence Ontology terms.
Selected Transcript Gene	Gene symbol of the selected transcript.
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	Consequences of the variant across all transcripts, in Sequence Ontology terms.

\

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.