Side bar: Variant list and quick classification (ANALYSES only)
The variants in your sample (ANALYSES mode) are listed in the side bar to the left:
Names (variant HGVSc and gene) and inheritance is displayed as specified by the default transcript in the gene panel. If there is more than one default transcript, all versions are shown.
Some variants have been automatically filtered from view before you start an analysis. These variants are still accessible via a button at the top of the variant list:
In this particular sample, there are a total of 3407 filtered variants, and none of these have been added back manually to the analysis by the user. Pushing the button brings up a window where you may select individual variants and add them back to the analysis:
The filters are configured to your user group/gene panel, but usually include, in this order:
FREQUENCY: Variants with a population frequency above the threshold for neutral variants (ACMG criterion BA1), predefined for the corresponding gene in the gene panel
REGION: UTR variants outside c.-20/c*20, intron variants outside +6/-20, and other, custom regions defined outside the scope of analysis. Variants are not excluded if they are annotated with a “worse” consequence than UTR/intron in an alternative RefSeq NM_ transcript for that gene.
QUALITY: Variants not meeting minimum quality criteria (if set).
SEGREGATION: Most of these filters are relevant for trio/family data only (joint called), except the last. These filters includes variants that are not:
- De novo (family).
- Autosomal recessive homozygous (family).
- X-linked recessive (family).
- Compound heterozygous (family).
- Single, non-filtered variant in a gene with automsomal recessive inheritance, except if loss-of-function.
In addition, there may be other filters, depending on the configuration of your user group/gene panel. Examples:
POLYPYRIMIDINE: Variants 1-2 nt in the intronic polypyrimidine tract (-20,-3) that only involve changes to/from pyrimidines (C/T)
CONSEQUENCE: Synonymous variants
Instead of performing a full classification, you may instead choose to use the Quick classification mode by pressing the button at the top of the variant list:
This feature is particularly well suited for workflows with large gene panels and many variants. The Quick classification view gives a summary of the most important information necessary for marking variants as
Not relevant (see Mark as verified/technical/not relevant), or classifying as
Class U or
Class 2 (see Set variant class), and gives you buttons to perform those actions directly:
Clicking one of these buttons moves the variant down to the respective section in the sidebar. If applicable, add a comment in the EVALUATION column before moving to the next variant.
When you are done, and ready to do a more thourough interpretation of any remaining variants, click the FULL CLASSIFICATION button at the top of the variant list (see also Evidence sections and Classification section)
If applicable, variants in the variant list are tagged with:
SSegregation. Depdending on data, changes to:
AAutosomal recessive homozygous
Shaded background: More than one variant in the same gene (in current sample)
Hold the mouse cursor over a tag to see the full label.
The default sorting of this list is Inheritance – Gene – HGVSc. You can change the sorting by clicking on any of the list headers:
- First click sorts descending (↓)
- Second click sorts ascending (↑)
- Third click returns to default sort
Existing and new classifications
Existing or newly set classes are given in the right-most column:
An arrow (→) indicates that a new classification will be created, and any existing class is given to the left of the arrow. If this classification is also outdated (long since last interpretation), an
* is added to the existing class.
Outdated variants marked with
* in CLASSIFIED VARIANTS should be re-interpreted before you finish the analysis.
Mark as reviewed
You can toggle a blue colouring of the background of the class by clicking on it in the side bar:
This can be used to indicates which variants have been reviewed, i.e. to keep track of the work done in a review round.