In the Variant Filter Builder, how can the “Value” field be used to apply filters to search for variants that have a 4/5 or pathogenic Community ranking?

The Variant Filter Builder is a cross functional tool that allows you to create and apply custom filters to variants based on different operators / variables and built-in rules, including the ability to set custom thresholds.

For example, when setting a custom threshold for the pathogenic community value:

– Add “level:count”. Here, the “level” refers to the pathogenicity flag, while the “count” refers to the number of times that this variant has been flagged as such.

If you already know the number of times that a specific pathogenicity flag has been used, you can use a definitive number with the setting of “MATCHES WITH”.

– Example: a variant that has been flagged as pathogenicity level 4, three times by the community. You will then add the following to the value field 4:3

If you do not know the number of times that a specific pathogenicity flag has been used, you can make use the wildcard symbol “*” which represents “anything”

– Example: a variant that has been flagged as pathogenicity level 5, multiple times by the community. You will then add the following to the value field 5:*

If you would like to add multiple values, these can be added and separated by a comma.

– Example: a variant that has been flagged as pathogenicity level 4, three times by the community OR a variant that has been flagged as pathogenicity level 5, multiple times by the community 4:3, 5:*

For detailed instructions please refer to the Operation Manual Section 5.

See screenshots to illustrate this filter.

csm screenshot 1
csm screenshot 2