Classification Flags

Each classification flag indiciates that there is an action that needs to be performed against the classification.

Many of the flags will be automatically raised by Shariant, though you will be able to open some of them yourself.

To look at the details of a specific open flag, simply click on it to be taken to the flag dialog.

Flag Dialog

../_images/flag_dialog.png

From the flag dialog, you can view summaries about what flags are currently open, see a list of flags that have been resolved as well as raise new ones. Note that only important flags still show up when closed, e.g. suggestions and internal reviews.

In the provided screenshot, we can see that we have an open flag asking us to share the classification, a completed internal review, an accepted suggestion and a rejected suggestion, as well as the buttons to create new internal reviews and suggestions.

You can visit the details of an open flag or a closed one by clicking on the icon.

From the details page of an open flag, depending on the type of flag, you can add a comment and potentially change the status of a flag.

You can raise a new flag by clicking on icons that have a “plus” button near the bottom of the dialog.

(The kinds of actions you can take on flags will depend on if you’re looking at a classification from your lab or another lab.)

See below for flags and how to solve them:

Flag Types

../_images/discordance.png Discordance

This classification is in discordance with one or more classifications.

  1. Ensure that you have completed an internal review of your lab’s classification recently (within the last 12 months is recommended). If not, raise the internal review flag and complete an internal review of your lab’s classification.

  2. Review any outstanding suggestions against your lab’s classification.

  3. View the other classifications in the discordance report and view the evidence differing between multiple records via the diff page. If appropriate, raise suggestions against other lab classifications.

  4. This Discordance flag will automatically be closed when concordance is reached.

This is discussed in the Classification Discordance page.

../_images/work.png Internal Review

This classification is marked as currently undergoing internal review.

  1. Once the internal review is complete, ensure you update the classification in your curation system.

  2. Mark the internal review as Completed.

This is discussed in the Classification Discordance page.

../_images/not-found.png Matching Variant

This classification is not yet linked to a variant

  1. If this has a status of In Progress we should match it to a variant shortly and no action is required.

  2. If this has the status of Matching Failed, we were unable to normalise the variant provided based on the c.hgvs and genome build values. Please contact Shariant support for help in resolving this.

../_images/matching-warning.png Matching Warning

The c.hgvs imported and the c.hgvs made after normalised by Shariant differs. This classification has been matched to a variant, but requires a manual check to ensure it was matched correctly

  1. If you believe it was matched correctly, select a status of Variant Confirmed and Save

  2. If you believe this is not the variant inteded, select a status of Variant Rejected and Save. An admin will then attempt to fix the problem.

../_images/outstanding_edits.png Outstanding Edits

Edits have been made to this classification that are not included in a published version.

  1. From the classification form, ensure there are no validation errors stopping this record from being published.

  2. At the bottom of the form, click the tick to submit the outstanding changes.

../_images/exchange.png Significance Changed

This classification has changed its clinical significance compared to a previously published version.

  1. Set the status of this flag to reflect the primary reason behind the change in classification.

  2. Please add a comment providing some context.

This is discussed in more detail on the Classification Discordance page.

../_images/lightbulb.png Suggestion

Someone has raised suggestion(s) against this classification.

  1. Review the contents of each suggestion.

  2. If appropriate, make changes in your curation system and mark the suggestion as Complete.

  3. If you decline the suggestion, mark it as Rejected.

../_images/lock.png Unshared Classification

This classification is not yet shared outside of your lab or institution.

  1. From the classification form, ensure there are no validation errors stopping this record from being published.

  2. Review the content of the classification to make sure it’s ready to be shared.

  3. At the bottom of the form, click the “Share” button to submit at a higher share level.

../_images/trash.png Withdrawn

This classification has been marked as withdrawn. It will be hidden from almost all searches and exports.

  1. If the classification is not of high enough quality or in error, you may leave it as “withdrawn” indefinitely.

  2. If you wish to un-withdraw the classification, click the open bin icon in actions from the variant classification form. (Note you can’t open a Withdrawn flag, but you can Withdraw/Unwithdraw from the classification form)