Interpret a Variant
Add an existing variant interpretation record (assertion) from knowledge bases to the report or create new assertions. When you create an assertion, Connected Insights provides reference information. Create an assertion as follows.
Navigate to the Biomarker Details panel.
Select Create New Assertion to add new assertion information based on the criteria in the following fields.
After the information is added, select Save & Add to Report.
[Optional] To cause the variant to appear in the Hereditary Risk Findings section of the report, select the Also report as a hereditary risk finding? checkbox.
Level
The following assertion levels are only available for variants.
Field Name
Description
Assertion Level
Description
Nucleotide
Assertion is established for the specific genome build, chromosome, position, reference allele,alternate allele, available for small variants with transcript annotation.
Amino Acid
Assertion is established for the specific amino acid and is available for small variants with HGVSP annotation.
Codon
Assertion is established for the specific codon and is available for small variants with HGVSP and missense consequence annotation.
Exon
Assertion is established for the specific exon and is available for small variants and copy number variants with exon annotation.
Gene
Assertion is established for the specific gene and is available for small variants with gene annotation.
Annotation Overlap
Assertion is specific to the genome build and genomic range and is available for large variants and RNA splice variants.
Partial Fusion
Assertion is specific to at least one of the genes and is available for RNA fusion variants.
Exact Fusion
Assertion is established for the specific gene, fusion gene, and fusion directionality. This assertion uses available structural variants and RNA fusion variants with a fusion gene.
Consequences
Consequences allow more accurate descriptions of the applicability of an assertion. For example, if you are creating an assertion for an EGFR exon 19 deletion, the assertion can be specified as follows.
Level = Exon
Consequence = Inframe deletion
This means that the assertion is applicable to any EGFR exon 19 deletion, regardless of the specific nucleotide change.
For biological assertions, if the gain of function variant or loss of function variant is added, this variant is annotated with these consequences in future cases or if you refresh the case assertions. If a variant is annotated with these consequences, then the relevant assertions are shown (for example,evidence for activating mutations). The following consequences are available:
Gain of function variant
Loss of function variant
Selected transcript consequences
When you match assertions to variants, the Consequences field is matched using OR logic. For example, if an assertion has the stop gained, start lost,and frame shift variant consequences, it can be matched to any variant that has at least one of those consequences.
Type
Field Name
Description
Type
Description
Biological
The pathogenicity of the variant that is available for variants.
Therapeutic
Relating to the treatment of disease or disorders by remedial agents or methods.
Prognostic
Provides information about the overall cancer outcome of the patient, regardless of the therapy.
Diagnostic
The process for identifying a disease, condition, or injury from its signs and symptoms.
Direction
These directions are for the therapeutic type.
Field Name
Description
Direction
Description
Responsive
Having to do with a good response or improvement in relation to the treatment.
Non-Responsive
Having to do with poor response associated with the treatment.
Contraindicated
A drug or treatment that must not be used in a particular situation, as it is likely to harm the patient.
Therapy
Search for drugs by RxNorm term. Therapy is available for the therapeutic type. For combination drug assertions, select more than one drug in the same assertion. For single drug assertions, select a single drug per assertion.
Disease
Search for diseases by SNOMEDCT term. The disease defaults to the disease of the case.
Classification
Specify the classification. For therapeutic, prognostic, and diagnostic, Illumina Pre-Configured Tiering is based on Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. Set up your own classifications following the guidance in Custom Actionability Classification. For biological, these sections are Pathogenic, Likely Pathogenic, VUS, Likely Benign, and Benign.
Status — Specify high or low. The status is available for TMB, MSI, and GIS.
HRD — Specify high or low. HRD is available for GIS and variants when the selected transcript is for BRCA1/2.
Summary — Provides a free text field for adding a summary to the assertion. These summaries are intended to be shown in the reportPDF.
Notes — Provides a free text field for adding notes to the assertion. These notes are not intended to be shown in the report PDF.
Gene Description
Specify the role and summary.
Role — The gene role can be Ocongene, Tumor Suppressor, or both.
Summary — Provides a free text field for adding a summary to the assertion. These summaries are intended to be shown in the reportPDF.
Clinical Trials
Specify the following information:
Level — For more information, refer to Level.
Consequences — For more information, refer to Consequences.
Registry — The registry of the clinical trial (for example, CTGov).
Registry ID — The registry identifier (for example, NCT1234).
Phase — The phase of the clinical trial (for example, Phase III).
External Link — The URL for the clinical trial.
Disease — For more information, refer to Disease.
Location — The city, state, and country of the clinical trial. Multiple locations can be added, and only country is required.
HRD
Specify high or low. HRD is available for GIS and variants when the selected transcript is for BRCA1/2.
Summary
Provides a free text field for adding a summary to the assertion. These summaries are intended to be shown in the report PDF.
Notes
Provides a free text field for adding notes to the assertion. These notes are not intended to be shown in the report PDF.
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