> For the complete documentation index, see [llms.txt](https://help.bioinsight.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.bioinsight.illumina.com/connected-insights/interpret-and-report/viewdetails-introduction/viewdetails-variant-overview.md).
# Variant Overview
This section provides details about the variant call and is only available for variant biomarkers.
### Common Information
| **Field Name** | **Description** |
| ---------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| 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. |
| VCF Position | The position (POS) as annotated in the VCF. |
| VCF Ref Allele | The reference allele (REF) as annotated in the VCF. |
| VCF Alt Allele | The alternate allele (ALT) as annotated in the VCF. |
| HGVSg | HGVSg nomenclature of the variant. |
| Length | Length of the variant in base pairs. |
| Cytogenetic Band | Cytoband of variant. |
| ISCN | ISCN nomenclature. |
| Predicted Origin | Predicted origin of the variant (e.g. Somatic, Germline, or CHIP). Refer to [Predicted Origin](https://github.com/illumina-swi/ici-docs/tree/main/docs/interpret-and-report/viewdetails-introduction/avf-introduction/avf-variant-details-filters.md#predicted-origin). |
| HGVS (Transcript) | HGVSc and HGVSp (in both 3-letter and 1-letter form) change of the variant on the selected transcript. |
| Exons (Transcript) | Impacted exon(s) (numerator) and total number of exons on the selected transcript (denominator). |
| Introns (Transcript) | Impacted intron(s) (numerator) and total number of introns on the selected transcript (denominator). |
| Consequences (Transcript) | Consequences of the variant on the selected transcript, in Sequence Ontology terms. |
| Gene (Transcript) | Gene symbol of the selected transcript. |
| All Transcript Consequences (Transcript) | Consequences of the variant across all transcripts, in Sequence Ontology terms. |
> **Note:** Additional details present in the INFO fields of the variant from the VCF will also be displayed here.
### 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. |
### Sample Metrics
| **Field Name** | **Description** |
| ---------------- | ----------------------------------------------------------------------------------------------------------------- |
| VCF Filters | The variant filters associated to this variant (FILTER) as annotated in the VCF. |
| Somatic Quality | Somatic quality of the variant for each sample (SQ). |
| VAF | The variant allele frequency for each sample. Calculated from (allele depth or supporting reads) / (total depth). |
| Genotype | The genotype of the variant for each sample (GT). |
| Allele Depth | The allele depth of the variant for each sample (AD). |
| Total Depth | The total depth of the position of the variant for each sample (DP). |
| Fold Change | The fold change of the variant for each sample (FC or SM). |
| Copy Number | The copy number of the variant for each sample (CN). |
| Paired Reads | The paired reads of the variant for each sample (PR). |
| Split Reads | The split reads of the variant for each sample (SR). |
| Supporting Reads | The combined supporting reads of the variant for each sample (VF or sum of PR and SR if VF not present). |
> **Note:** Additional details present in the FORMAT/SAMPLE fields of the variant from the VCF will also be displayed here. The value shown will correspond to the allele, when possible (i.e. Number=R or Number=A).
---
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