Variants Tab

The variant grid can be found under the Variants tab within a case. Each tab represents a filtered list of the variants, and each row contains data for one variant. The data include biological information associated with the variant in various annotation sources. The variant grid provides a set of tools to sort, filter, flag, and review variants.

By default, the page displays a list of variants that meet the criteria of the filter configured in the test definition. Adding new filters creates additional tabs, with each having a list of variants meeting the criteria of the corresponding filters. For more information about applying filters, refer to Apply Variant Filters.

The following table lists the contents of each column in the variant grid.

Variant Grid Columns

Column Header	Description
Interpret	Selecting Interpret allows you to open a Biomarker Details page for that variant to review additional information and perform variant interpretation. After an assertion for this variant has been created for this case, this button lists the highest actionability category for this variant in this case.
Flag	Allows you to add to the variant a flag with a custom label and color. These flags can be configured in Test Components and can help facilitate variant review. The flags can be used for variant filtering. More than one flag can be added per variant.
IGV	Selecting IGV opens the Integrative Genomics Viewer (IGV) that can be used to view the sequenced reads at the variant position.
My Knowledge Base (sortable)	This label indicates the following information: Highest biological classification across all diseases Highest actionability classification across the following: • Diagnostic classifications for all diseases • Prognostic classifications for case and ancestor diseases • Therapeutic classifications for case and ancestor diseases When sorting by this column, variants are ordered by highest classification between biological classification and actionability. If updated assertions for the case disease have been detected, a notification displays in the case header. You can choose to refresh this column with the latest content.
Other Knowledge Bases (sortable)	This label indicates the following information based on UMLS-DO and UMLS-OncoTree disease mapping: Highest OncoKB biological classification across all diseases Highest OncoKB actionability classification across the following: • Diagnostic classifications for all diseases • Prognostic classifications for case and ancestor diseases • Therapeutic classifications for case and ancestor diseases Highest CKB actionability classification across the following: • Diagnostic classifications for all diseases • Prognostic classifications for case and ancestor diseases • Therapeutic classifications for case and ancestor diseases Highest CIViC actionability classification across the following: • Diagnostic classifications for all diseases • Prognostic classifications for case and ancestor diseases • Therapeutic classifications for case and ancestor diseases When sorting by this column, variants are ordered first by OncoKB (using highest classification between biological classification and actionability), then by CKB, and finally by CIViC. If updated assertions for the case disease have been detected, a notification displays in the case header. You can choose to refresh this column with the latest content.
COSMIC (sortable)	The maximum number of samples with the given variant reported in COSMIC. If the variant has a corresponding record in the COSMIC database, and there are multiple COSMIC entries, the sample size associated with the COSMIC entry with the largest sample size is shown.
Genes	Lists a gene or genes in which the identified variant occurs. Genes, HGVS notations, transcripts, consequence, and other transcript-related variant details are provided for the "default transcript" selected for each variant.
LOH Overlap	Indicates that the small variant overlaps with a call of LOH.
CGC (sortable)	The gene role from COSMIC Cancer Gene Census. This information is specific to the gene from the selected transcript.
Consequences	The impact a variant has on the gene transcripts, such as missense or frameshift. Select More to view a summary of consequences for the variant across all transcripts.
HGVS / ISCN	For small variants, this shows the HGVSc and HGVSp (in both 3-letter and 1-letter form) nomenclature. For other variants, except for copy number neutral and RNA splice variants, this shows the ISCN nomenclature.
Cancer Hotspots (sortable)	The number of samples at the given hotspot in Cancer Hotspots. This information is specific to the Human Genome Variation Society (HGVS) of the selected transcript. Additional samples for other transcripts are indicated in parentheses.
Pop freq (sortable)	The highest population variant frequency in gnomAD (small variants) or the 1000 Genome Project (structural variants and copy number variants) represented as values from 0 to 1.
VAF (sortable)	Variant Allele Frequency. The proportion of reads supporting the alternative allele, represented as values from 0 to 1.
Origin	Indicates whether a variant is Suspected Somatic or Predicted Germline. For tumor-only analyses, when enabled in DRAGEN, the variant origin is determined for small variants based on population frequency databases. For tumor-normal analysis, when enabled in DRAGEN, the variant origin is determined for small variants or structural variants based on the presence or absence of the variant in the normal sample.
Position (sortable)	Chromosome number and variant position.
Change	Reference and alternative alleles for small variants (for example, Fold change, absolute copy number, and LOH in case of copy number variants, when available). LOH is determined by a minor copy number (MCN) of 0 for copy number variants with an absolute copy number (CN)greater than 0.
Quality (sortable)	The quality score reported by the secondary analysis pipeline.
ClinVar (sortable)	Interpretation categories of VCV entries (aggregate variant records) and RCV entries (aggregate variant-disease records) from ClinVar database. • Pathogenic (P) • Likely pathogenic (LP) • Unknown significance (VUS) • Likely benign (LB) • Benign (B)
Category (sortable)	Variant category (small variant, structural variant, copy number variant, RNA splice variant, orRNA fusion variant).
Transcript	Transcript identifier from RefSeq or Ensembl databases.
OMIM (sortable)	The mode of inheritance reported in OMIM. Highlighted values correspond to the gene of the selected transcript.
Cytoband (Sortable)	The cytoband location.
Variant Type	Variant type (SNV, insertion, deletion, and others).
Exons	Exon or range of exons affected by the variant followed by the total number of exons.
VCF Filters (sortable)	Value provided for the variant in the FILTER column of the VCF file. Refer to the variant call documentation to confirm possible values and recommended thresholds.
Length (bp) (sortable)	The length of the variant in bp.
pLI (sortable)	The score applies to the selected transcript. If the score is different across transcripts, the highest score is displayed in parentheses after the score for the selected transcript. For more information, refer to Acronyms and Terms.
SpliceAI (sortable)	The score can be interpreted as the probability of the variant being splice-altering. For more information, refer to Acronyms and Terms.
PrimateAI (sortable)	A deep residual neural network for classifying the pathogenicity of missense mutations. The score applies to the selected transcript. If the score is different across transcripts, the highest score is displayed in parentheses after the score for the selected transcript. For more information, refer to Acronyms and Terms.
PrimateAI-3D (sortable)	A three-dimensional (3D) convolutional neural network for classifying the pathogenicity of missense mutations. The score applies to the selected transcript. If the score is different across transcripts, the highest score is displayed in parentheses after the score for the selected transcript. For more information, refer to Acronyms and Terms.
PhyloP Score	This score measure evolutionary conservation at individual alignment sites. For more information, refer to Acronyms and Terms.
Allele Count (sortable)	Alternative allele counts in the gnomAD database.
Homozygote Count (sortable)	Number of individuals homozygous for alternate allele in the gnomAD database.
Hemizygote Count (sortable)	Number of individuals hemizygous for alternate allele in the gnomAD database.
Allele Depth	Number of reads supporting the variant call.
Total Depth	Number of reads aligned to the position of the variant call.
Split Reads	Number of reads supporting the variant call spanning the breakpoint.
Paired Reads	Number of reads supporting the variant call with paired ends supporting the breakpoint.
Supporting Reads	Number of reads in total supporting the breakpoint.
Gene Expression (TPM)	Gene expression is shown in transcripts per million (TPM) if provided by the secondary analysis pipeline (e.g., DRAGEN RNA).
Custom Annotation	Refer to Custom Annotations.