Below is an example of the step-by-step procedure to link a publication to a variant, classify a variant or provide a comment on a variant of your interest.
Linking a publication to a variant
In this example, we will be using the variant ATM:c.1464G>A. First, click on the “Publications” tab and then on “Link a publication”
This will bring up the pop-up shown below. Enter the PubMed ID or DOI of the publication you want to link and click on “Find”. Please note that although DOIs are supported, PubMed IDs work more reliably.
Once the publication has been found, you will be given the option to mark it as coming from a functional study (this is then used for ACMG rules PS3 and BS3) and also to claim authorship if you are one of the paper’s authors. Please make the relevant selections (if appropriate) and then click on Next:
In the next screen, you can choose to associate more variants to the same publication, and you can also choose whether the paper you are linking is referring to the variant as found in hg19 or hg38.
Next, you are asked to add supporting information about this variant, mentioned in or derived from the article, such as the claimed pathogenicity, or the mode of inheritance. Once you have made the relevant selections, you can click on Next:
Before you finish, you are given the opportunity to add (if mentioned in the publication) related phenotypes (All or OMIM) linked to the variant:
Finally, you have the option to share a comment and/or end the process. A comment, although optional, is often very helpful since you can add any detail from the paper that will help other users understand the variant in context.
Now the publication you have linked to the variant will be added to the "Publications" section. Other users may want to connect with you and comment on your entry (1), classify the variant (3) or if they agree with your linked publication they can click on "Like" icon (4).
If there are any changes you would like to make, you have the option to edit your entry anytime.
Also, you can link a publication or classify a variant by clicking on the options in the top page menu and then follow the instructions as described earlier:
How can I classify a variant?
As mentioned earlier, in the top page menu tab you can click on the “Classify" button.
This will bring the pop-up window shown below. You should carefully select a classification for the variant and optionally add supporting evidence for the claimed pathogenicity, such as additional variant information, or associated phenotype. It is strongly recommended when additional information is not provided as described above, to add a comment for this classification (not shown in picture below). Then, click on the Finish button.
How can I add a comment?
You can click on the "Community contributions" tab, where you can add your public comment about the variant and other users can view it interact with you on it.
If additional help is needed you can always email us at support@varsome.com. Thank you very much for your contribution!