Variant Details Filters

This page summarizes filters related to variant details. Filter availability can vary depending on the selected variant categories. If filters are applied to more than one variant category in the same condition group, only filters relevant for all variant categories are available. For more information, refer to Filter by Variant Category.

Origin

Filters variants by Suspected Somatic or Predicted Germline origin.

You can select these options when creating or editing a variant filter by updating the Origin criterion. For example, if you do not want predicted germline variants, then add or update the Origin criterion to only include Suspected Somatic. For more information, refer to Variant Filters.

You can also add or edit a test definition to include either somatic or predicted germline variants through selecting the applicable variant filters in the Variant Filter(s) field. For more information, refer to Test Definition Setup.

For tumor-only analyses, when enabled in DRAGEN, variant origin is determined for small variants based on population frequency databases.

For tumor-normal analysis, when enabled in DRAGEN, variant origin is determined for small variants based on the presence or absence of the variant in the normal sample.

LOH Overlap

Filters small variants by overlap with an LOH event when LOH data is provided.

Genes

Filters variants by genes. There are two ways to create gene lists in the filter.

• Using a list of gene names. To create a gene list, type or paste gene names in the Additional Genes field.

• Using gene-disease associations from several sources. For more information, refer to Disease Association Filters.

Variant Type

Filters small variants, structural variants, and copy number variants by their types.

❗ The variant type is only selectable in a filter group with a single selected variant category as the variant types are tied to specific variant categories.

Consequences

Filters data by specific consequences.

❗ The consequence filter is only selectable in a condition group with a single selected variant category as the consequences are tied to specific variant categories.

Small Variant Consequences

When annotating transcripts with terms, Connected Insights uses the most specific term supported by the variant annotator.

Consequence filters return only the specified term and do not automatically include child terms. Specify the exact terms to include in the filter results.

Functional Consequences

Consequence	Description
Gain of Function Variant	The variant results in gain of function.
Loss of Function Variant	The variant results in loss of function.

These consequences are annotated when a variant has a biological assertion from any source with these consequences (for example, JAX-CKB or MyKnowledge Base).

Coding Sequences

Start and Stop Alterations

Filters data by the presence and location of start and stop alterations.

Start and Stop Alterations

Consequence	Description
Start Loss	The loss of a start codon in the coding sequence.
Stop Gained	The gain of a stop codon in the coding sequence.
Stop Loss	The loss of a stop codon in the coding sequence.
Incomplete Terminal Codon	A change to at least one base of the final codon of an incomplete annotated transcript.
Feature Elongation	The variant causes the extension of the genomic feature.
Feature Truncation	The variant causes the reduction of a genomic feature.

Splice Site

Filters data by the affected splice site.

Type	Description
Splice Acceptor Variant	The variant affects the canonical splice acceptor site (last two bases of the 3' end of the intron).
Splice Donor Variant	The variant affects the canonical splice donor site (first two bases of the 5' of the intron).
Splice Region Variant	An indel or substitution in a non coding splice region of the gene.

Indels

Type	Description
Frameshift Variant	An insertion or deletion in which the number of base pairs is not divisible by 3, causing a frame disruption.
Inframe Deletion	A deletion that does not disrupt the reading frame.
Inframe Insertion	An insertion that does not disrupt the reading frame.

Other

Type	Description
Missense Variant	A single base pair substitution that results in the translation of a different amino acid at the position.
Protein Altering Variant	The variant has a protein-altering coding consequence.
Coding Sequence Variant	The variant changes the coding sequence.

Silent Consequences

Filters data by the variant relationship to a gene.

Type	Description
Intergenic Variant	The variant position is not covered by any gene transcript.
Upstream Gene Variant	The variant position is within 5 kb upstream of the defined transcript start coordinate.
Downstream Gene Variant	The variant position is within 5 kb downstream of the defined transcript end coordinate.
Intron Variant	The variant occurs within an intron region.
3-prime UTR Variant	The variant is in the 3' untranslated region of a gene.
5-prime UTR Variant	The variant is in the 5' untranslated region of a gene.
Noncoding Transcript Exon Variant	The variant changes the noncoding exon sequence in a noncoding transcript.
Noncoding Transcript Variant	The variant occurs in a noncoding RNA gene.
Synonymous Variant	The variant does not affect the primary amino acid sequence of the translated protein.
Start Retained Variant	At least one base in the start codon is changed, but the start codon remains.
Stop Retained Variant	At least one base in the terminator code is changed, but the terminator remains.
Mature miRNA Variant	The variant occurs within a mature miRNA sequence.
NMD Transcript Variant	The variant is in a transcript and is the target of nonsense-mediated decay (NMD).
Regulatory Region Ablation	A deletion of a region that contains a regulatory region.
Regulatory Region Amplification	An amplification of a region that contains a regulatory region.
Regulatory Region Variation	The variant occurs in a regulatory region.

Structural Variant Consequences

When annotating transcripts with terms, Connected Insights uses the most specific terms supported by the variant annotator. Consequence filters return only the specified term and do not automatically include child terms. Specify the exact terms to include in the filter results.

Functional Consequences

Consequence	Description
Gain of Function Variant	The variant results in gain of function.
Loss of Function Variant	The variant results in loss of function.

These consequences are annotated when a variant has a biological assertion from any source with these consequences (for example, JAX-CKB or MyKnowledge Base).

Transcript Consequences

Filters data by the transcript consequence.

Consequence	Description
Transcript Variant	The variant changes the structure of the transcript.
Intron Variant	The variant is completely within the intron region of the gene.
Exon Variant	The variant is completely within the exon region of the gene.
Transcript Ablation	A deletion of the region that contains a transcript feature.
Transcript Amplification	An amplification of a region that contains a transcript.
Feature Elongation	The variant causes the extension of a genomic feature.
Feature Truncation	The variant causes the reduction of a genomic feature.
5-Prime Duplicated Transcript	A partially duplicated transcript in which the 5' end of the transcript is duplicated.
3-Prime Duplicated Transcript	A partially duplicated transcript in which the 3' end of the transcript is duplicated.

Gene Fusion Consequence

Filters data by the gene fusion consequence.

Consequence	Description
Unidirectional Gene Fusion	A fusion of two genes on the same strand.
Bidirectional Gene Fusion	A fusion of two genes on the opposite strand.
Gene Fusion	A fusion of two genes with ambiguous or unknown strand.

Copy Number Variant Consequences

When annotating transcripts with terms, Connected Insights uses the most specific term supported by the variant annotator. Consequence filters return only the specified term and do not automatically include child terms. Specify the exact terms to include in the filter results.

Consequence	Description
Gain of Function Variant	The variant results in gain of function.
Loss of Function Variant	The variant results in loss of function.

These consequences are annotated when a variant has a biological assertion from any source with these consequences (for example, JAX-CKB or MyKnowledge Base).

Transcript Consequences

Filters data by the transcript consequence.

Consequence	Description
Transcript Variant	The variant changes the structure of the transcript.
Intron Variant	The variant is completely within the intron region of the gene.
Exon Variant	The variant is completely within the exon region of the gene.
Transcript Ablation	A deletion of a region that contains a transcript feature.
Transcript Amplification	An amplification of a region that contains a transcript.
Transcript Truncation	A truncation of a region that contains a transcript.
Feature Elongation	The variant causes the extension of a genomic feature.
Feature Truncation	The variant causes the reduction of a genomic feature.
5-Prime Duplicated Transcript	A partially duplicated transcript in which the 5' end of the transcript is duplicated.
3-Prime Duplicated Transcript	A partially duplicated transcript in which the 3' end of the transcript is duplicated.
Loss of Heterozygosity	The variant results in loss of heterozygosity of the transcript.

Copy Number Variant Consequence Filters

Filters data by the copy number consequence.

Type	Description
Copy Number Increase	The copy number is increased relative to the reference sequence.
Copy Number Decrease	The copy number is decreased relative to the reference sequence.
Copy Number Change	The copy number is increased or decreased.
Intron	The variant is completely within the intron region of the gene.
Exon	The variant is completely within the exon region of the gene.

RNA Splice Variant Consequences

Consequence	Description
Gain of Function Variant	The variant results in gain of function.
Loss of Function Variant	The variant results in loss of function.

The functional consequences are annotated when a variant has a biological assertion from any source with these consequences (for example, JAX-CKB or My Knowledge Base).

RNA Splice Variant

Consequence	Description
Exon Loss Consequence	A loss of one or more exons in a gene.

RNA Fusion Variant Consequences

Consequence	Description
Gain of Function Variant	The variant results in gain of function.
Loss of Function Variant	The variant results in loss of function.

The functional consequences are annotated when a variant has a biological assertion from any source with these consequences (for example, CKB or My Knowledge Base).

RNA Splice Variant

Consequence	Description
Unidirectional Gene Fusion	A fusion of two genes on the same strand.
Transcript Variant	The variant changes the structure transcript.

Position (Chromosome)

Filters by specified chromosomes. If no chromosome is selected, the chromosome filter is not applied.

Position (Genomic Regions)

Filters by specified regions. The input format is chr#: start-stop, within multiple regions separated by spaces or new lines.

Change (Copy Number)

These values indicate a reference, deletion, or amplification of copy number variants.

❗ The change (copy number) filter is only selectable in a condition group with only the copy number variant category.

Change (Fold Change)

With copy number variants, the fold change value is derived from the normalized read depth of the gene in a sample. This depth is relative to the normalized ready depth of diploid regions in the same sample.

❗ The change (fold change) filter is only selectable in a condition group with only the copy number variant category.

Length

Filters data by variant length with resolution up to one bp.