FAQs varSEAK

General

I have been on www.varSEAK.bio and it is just a database. What is the difference between www.varSEAK.bio („varSEAK Online“) and varSEAK Pilot?

The www.varSEAK.bio website offers free and public access to the varSEAK database. The varSEAK variant database comprises numerous public databases including direct links, eliminating the need for laborious searches. On top of that, varSEAK offers ACMG conform classifications submitted by genetic professionals using the varSEAK Pilot or varSEAK Open software module.

The varSEAK Pilot software module can be seamlessly integrated into your SEQUENCE Pilot workflow. It serves to conveniently filter your orders, characterise and classify variants, including ACMG-criteria, HPO-conform phenotypes, descriptions, inheritance patterns, attached documents and weblinks. Moreover, varSEAK is designed as a communications network, simplifying making contact with other genetic experts for professional exchange.

Please refer to our Products page for more details.

Is varSEAK cloud-based?

varSEAK is not cloud-based. All patient data stays safe within the varSEAK Pilot or varSEAK Open installation inside the local network. All public database and varSEAK database information are stored on the varSEAK global server and can be queried from varSEAK Online, varSEAK Pilot or varSEAK Open. Therefore, it is necessary that the local varSEAK Pilot or varSEAK Open installation has permanent internet access to the varSEAK global server. For more details, please refer to Hardware Requirements for varSEAK.

How does the ‚varSEAK Classification‘ come about?

The varSEAK Classification is the average of the submitted classifications from the institutions using varSEAK Pilot or varSEAK Open. The value is given both as a word and in digits.

What do the numbers in the line below the varSEAK Classification mean?

The numbers serve to elucidate the occurrence of the varSEAK Classification: it shows how often each class has been submitted. Each position stands for one class, from class 1 (benign) on the left to class 5 (pathogenic) on the right. The numbers account for the varSEAK users having submitted the respective classification.

Example: (0/0/0/1/2) would mean that the variant has been classified as „likely pathogenic“ (class 4) by one varSEAK user and as „pathogenic“ (class 5) by two varSEAK users.

What data is submitted to the varSEAK database?

To request database information to be displayed in varSEAK Pilot, only the variant (chromosome, position, reference sequence, altered sequence) is used.

When submitting a variant, the sent data are: the variant (including transcript/HGVS nomenclature), its classification (ACMG classification tier only, no additional information) and the laboratory (as submitter). No patient or order related data is ever transferred to the global varSEAK database.

What does varSEAK cost?

varSEAK Online is publicly accessible and free of charge.

The locally installable varSEAK software (varSEAK Pilot, varSEAK Open, varSEAK Consortium) is available in several configurations. For a quote or price list, please contact our varSEAK support team.

I would like to try varSEAK. What do I need to do?

I would like a combined trial license of SEQUENCE Pilot and varSEAK Pilot:

Please use our contact form to request your free trial license.

I am already using SEQUENCE Pilot:

Please contact our varSEAK support team and let us know you are interested in a trial license. Please state your and your institution‘s/department‘s contact details so we can assign your request correctly.

I have another question…

Please contact our varSEAK support team - we are happy to help.

varSEAK Pilot
The entries in the column ‚My Classification‘ have different colours. What does this mean?

There are four possible colours for this field, representing four different meanings:
- blue: this classification was set by your laboratory, either in SEQUENCE Pilot or in varSEAK Pilot.
- Violet: this classification was set based on the field „MutEffect“ from SEQUENCE Pilot at the Import of your SEQUENCE Pilot mutation database.
- red, bold: this classification is not yet set, it is „unknown“. This is not to be confused with „uncertain significance“ (ACMG classification tier 3)
- orange, bold: this classification is also not yet set, but there is an automated suggestion based on identical entries of clinical significance for both ClinVar and ClinVitae.
Where can I find the new ACMG classification feature?

You can access it from any menu where you can add or edit a classification. The new function is accessible via the button [Add/Edit ACMG Classification] within the Add/Edit Classification modular window.

Where can I find the user manual?

The manual is linked in the footer of each page, on the left hand's side.
varSEAK Online
What is the difference between varSEAK Online and varSEAK Pilot or varSEAK Open?

Please refer to the General varSEAK FAQ above.
Where can I find more information about the Splice Site Prediction Tool?

When using the Splice Site Prediction Tool (you can also click the "Show Example" Button on the start page), you can find information in the "INFO" banner that can be folded out in the lower right corner of the screen. There you can find:
- the legend for the graphical display
- a link to the "Read me" file, which explains the displayed scores in more detail
- a link to the "Development & Validation" file, which explains how the Splice Site Prediction Tool was developed and validated.
  This file does also contain more examples.

varSEAK Pilot
varSEAK Online

The entries in the column ‚My Classification‘ have different colours. What does this mean?

There are four possible colours for this field, representing four different meanings:

blue: this classification was set by your laboratory, either in SEQUENCE Pilot or in varSEAK Pilot.
Violet: this classification was set based on the field „MutEffect“ from SEQUENCE Pilot at the Import of your SEQUENCE Pilot mutation database.
red, bold: this classification is not yet set, it is „unknown“. This is not to be confused with „uncertain significance“ (ACMG classification tier 3)
orange, bold: this classification is also not yet set, but there is an automated suggestion based on identical entries of clinical significance for both ClinVar and ClinVitae.

Where can I find the new ACMG classification feature?

You can access it from any menu where you can add or edit a classification. The new function is accessible via the button [Add/Edit ACMG Classification] within the Add/Edit Classification modular window.

Where can I find the user manual?

The manual is linked in the footer of each page, on the left hand's side.

What is the difference between varSEAK Online and varSEAK Pilot or varSEAK Open?

Please refer to the General varSEAK FAQ above.

Where can I find more information about the Splice Site Prediction Tool?

When using the Splice Site Prediction Tool (you can also click the "Show Example" Button on the start page), you can find information in the "INFO" banner that can be folded out in the lower right corner of the screen. There you can find:

the legend for the graphical display
a link to the "Read me" file, which explains the displayed scores in more detail
a link to the "Development & Validation" file, which explains how the Splice Site Prediction Tool was developed and validated.
This file does also contain more examples.