CaseLog

The filter labels list the studies and phenotypes where the variant is observed. Select one or more labels to view only results that match the label.

Show or hide variant types using the show/hide color legend.

The needle plot contains the following sections:

•

Allele Frequency—Allele frequencies of the observed variants.

•

A triangle marks the location of a specific variant. The marker appears when the Gene tab is opened from variant search results, or you can set a marker by clicking on the respective needle.

•

Needle height represents population frequency in the underlying cohort. Longer needles represent frequent variants.

•

Needle lines represent the data set the variant was found in. Solid lines represent data in your cohort and dashed lines represent variants in partner data sets.

•

Solid color bars on the x-axis represent the protein domain.

•

A tooltip contains details about the variant.

•

PrimateAI—Scores for potential missense variants that results from an SNV, based on common polymorphisms observed in other species of primates. The reported score is the average of all raw scores for variants at the same genomic location.

•

Dotted lines represent the 75th and 25th percentile of scores.

•

Points above the 75th percentile are considered likely pathogenic and points below the 25th percentile are considered likely benign.

•

Pathogenic variants—Pathogenic and likely pathogenic variants from your Knowledge Network database (represented by circles) or the ClinVar database (represented by triangles), color-coded by variant type. A tooltip contains variant details and a link to the ClinVar entry for the variant.

•

Exons—Exon boundaries and amino acid positions. To change the current zoom, drag the sliders on the left and right of the plot.

Data tables list the results of genetic burden tests and an overview of all observed variants.

•

Genetic burden test using de novo variants only—Compares the expected to the observed de novo mutation rate in a given gene for each phenotype, using data from all studies available.

•

Genetic burden test using all rare damaging variants rates—Compares expected to observed ratios of rare damaging variants and rare synonymous variants. TruSight Software considers the following variant types to be rare and damaging:

•

Variants with frequency < 0.1%.

•

All nonsense (stop-gained) and frameshift variants.

•

Missense variants with Primate AI scores above 75th percentile for the given gene.

•

Slice-site and intronic variants with Splice AI score > 0.2.

•

List of variants—Overview of all variants observed in the gene, including variants in non-coding regions. Includes CDS and protein changes if applicable, and the study the variant was observed in.

•

Enter a term in the search field to filter the list.

•

Select Export to CSV to download the list.

•

Select the variant ID to view variant data in the Variant tab.