> 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/inter-transcripts.md).
# Variant Transcripts
Connected Insights performs variant annotation and matches variants to the records in external knowledge bases and functional impact predictions based on a set of pre-selected default transcripts. Variant details, such as c.HGVS and p.HGVS labels and consequences, are also generated based on default transcripts.
In the current implementation, you can only change transcripts for specific variants.
View default transcripts as follows.
1. [Add the Transcript column](/connected-insights/interpret-and-report/inter-variant-grid/inter-modify-variant-grid.md) in the variant grid of the [Variants](/connected-insights/interpret-and-report/inter-variant-grid.md) page.\
The HGVS and Consequences columns provide variants c.HGVS and p.HGVS labels and consequences based on the default transcript. Selecting **More** in the Consequences column shows all consequences for the default transcript (left column) and all transcripts including the default one (right column).
2. Open the [Biomarker Details](/connected-insights/interpret-and-report/viewdetails-introduction.md) page by selecting **Interpret** on the [Overview](/connected-insights/interpret-and-report/cm-overview-tab.md) or [Variants](/connected-insights/interpret-and-report/inter-variant-grid.md) tabs.\
The default transcript is provided in the top-right corner.
3. Click the transcript button to view a list of transcripts that the variant impacts. A ☆ represents the default transcript, while a C represents the canonical transcript.
1. A searchable dropdown shows all genes for transcripts that the variant overlaps. Select a gene symbol to filter the transcripts.
## Default Transcript Selection
In Connected Insights, the following rules determine the default transcript:
1. If there are [preferred transcripts](/connected-insights/configure/configuration/c-preferred-transcripts.md) annotated for the given report, limit to the list of preferred transcripts for a given variant. If there are no preferred transcripts for the given variant, skip this step.
2. When present, limit to the collection of transcripts for a given variant that have assertions from any source. This step prioritizes transcripts by highest assertion actionability, then by the most specific assertion level.
3. If there are any transcripts with Gain of Function, Loss of Function, or Switch of Function consequences, limit to those transcripts.
4. Limit to the collection of transcripts for a given variant that are the highest tier by consequence based on the variant category.
5. If canonical transcripts are present, limit to canonical transcripts.
6. Limit to the genes in the key genes configuration for the case disease.
7. When present, limit to the genes that have the highest role classification from Cancer Gene Census (Oncogene > Fusion > TSG).
8. Select the gene that is first alphabetically.
9. If RefSeq and Ensembl transcripts are present, limit to RefSeq transcripts.
10. If there are multiple transcripts remaining, select the first transcript alphabetically.
Assertions include the following levels:
* Nucleotide
* DNA
* Amino Acid
* Codon
* Protein Range
* Exon
* Gene
* Annotation Overlap
* Exact Fusion
* Specific Fusion
* Partial Fusion
* Splice
The following variant categories define consequence tiers:
### Consequence Tiers that Define Default Transcripts Setup
| **Tier** | Small Variant | Copy Number Variant | Structural Variant or RNA Fusion Variant | RNA Splice Variant |
| -------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------ | --------------------------------------------- |
| 1 | • Start Loss
• Stop Gained
• Stop Loss
• Feature Truncation
• Frame shift Variant
• Splice Donor Variant
• Splice Acceptor Variant
| • Copy Number Decrease
• Loss of Heterozygosity
| • Inframe Unidirectional Gene Fusion
• Unidirectional Gene Fusion
• Frameshift Unidirectional Gene Fusion
| • Exon Loss Variant |
| 2 | • Incomplete Terminal Codon
• Feature Elongation
• Splice Region Variant
• Inframe Deletion
• Inframe Insertion
• Missense Variant
• Protein Altering Variant
• Coding Sequence Variant
| • Copy Number Increase
• Copy Number Change
| • Unidirectional Intergenic Fusion | • Any other undefined transcript consequences |
| 3 | • Intron Variant
• 5' UTR Variant
• 3' UTR Variant
• Non-coding Transcript Exon Variant
• Non-coding Transcript Variant
• Synonymous Variant
• Start Retained Variant
• Stop Retained Variant
• NMD Transcript Variant
| • Transcript Ablation
• Feature Truncation
• Feature Elongation
| • Bidirectional Gene Fusion | |
| 4 | • Upstream Gene Variant
• Downstream Gene Variant
• Mature miRNA Variant
• Regulatory Region Ablation
• Regulatory Region Amplification
• Regulatory Region Variation
• Any other undefined transcript consequences
| • Transcript Amplification
•Transcript Variant
• 5' Duplicated Transcript
• 3' Duplicated Transcript
| • 5' Gene Fusion
• 3' Gene Fusion
• Upstream Intergenic Fusion
• Downstream Intergenic Fusion
• Gene Fusion
| |
| 5 | | • Any other undefined transcript consequences | • Inframe Insertion | |
| 6 | | | • Transcript Ablation
• Feature Truncation
• Feature Elongation
| |
| 7 | | | • Transcript Amplification
• Transcript Variant
• 5' Duplicated Transcript
• 3' Duplicated Transcript
| |
| 8 | | | • Any other undefined transcript consequences | |
## Changing Transcripts
In the current version of Connected Insights, users can only change transcripts for specific variants. The transcripts can be viewed and updated in the top-right corner of the Biomarker Details page for a specific variant. Changing transcripts updates the information for this variant in the variant grid and in the Biomarker Details page content. These updates include assertions in the following sections that have transcript-specific content:
* My Knowledge Base
* Other Knowledge Bases
* Clinical Trials
* Computer Predictors
---
# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.
## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation by asking a question.
Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:
```
GET https://help.bioinsight.illumina.com/connected-insights/interpret-and-report/inter-transcripts.md?ask=&goal=
```
`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.
Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.