The ClinVar Submission Wizard

The ClinVar submission wizard is available through the Variation submission portal . It guides you through the steps of a submission to ClinVar. You can use the wizard for:

  • an interpretation of a single variant, compound heterozygote, or haplotype
  • an interpretation of a sequence or a structural variant
  • an interpretation relative to a disorder, a set of observed phenotypes, or a drug response
  • aggregate or individual observations as evidence
  • experimental evidence

The wizard does not handle all types of submissions. Please use our submission spreadsheets for the following cases:

  • if you have more than one interpretation to submit
  • an interpretation about a diplotype (a genotype of two haplotypes)
  • an interpretation about a translocation
  • any cytogenetic variant
  • an update to a previous submission

We will announce when the wizard supports these additional types of submissions.

General information

The steps that are part of the wizard are summarized by the tabs at the top of each page. If information is required, there is an asterisk (*) next to the label. Most fields have a (?) icon; if you hover over that you will find more information about how to use that part of the form.

For some types of content, you may want to enter multiple values. Click on the label next to the (+) icon to add more values. If you want to remove any you have added in error, click on (-) remove.

After you complete the information on any tab, click on the Save and Continue button the bottom of the page. If there was an error on that page, you will be prompted to correct your submission. At any time during the submission process, you can return to a previous tab, make edits, and then click Save and Continue to save your entries.

Table of contents

  1. Info

  2. Organization

  3. Variant
  4. Conditions
  5. Interpretation
  6. Observations
  7. Overview

Info

Use the fields on this tab to enter information about your submission as a whole. Note that by default, a submission identifier is automatically created (in this example SUB190600), and added as Name of your submission . You can edit this value to provide a name that is meaningful to you; it will display on your home page in the Submission Portal. However, this name is not included in your ClinVar record.

Most of the values on this tab are optional. Please do note that the default value for Release status is Public. If you wish to assign a hold on your submission, remember to change the selection. More about our release policy...

Citations

One or more citations may be entered related to your submission as a whole, or related to specific concept in your submission. Citations you enter on the Info tab are processed as related to the complete submission.

If you are submitting to ClinVar in advance of publication, please skip this field. When your paper is published, ClinVar staff will add your publications to your submission on your behalf.

If you have a database identifier for your publication (PubMed, PubMed Central, DOI, NCBI BookShelf), please select the name of the database from the menu, and add the database identifier to the Citation ID or text space. If there is no database identifier, please provide the citation as free text, including authors, publication date, source, and title.

ClinVar submission wizard, image of the info tab

Organization

To enter the organizations, and staff members from that organization who are submitting data, you must already have registered yourself as authorized to submit for that organization. If you have any questions about this process, please refer to the general help documents for the Variation Submission Portal.

Single submitter

If only one organization is the submitter, all you need to do is press Save and Continue. No additional entry is necessary.

Initial display in the Organization tab.

Multiple submitters

If, however, you are submitting for more than one organization, select Multiple organizations. A window will open listing all the organizations for which you are authorized to make a submission. Use this form to select the one that is primary, and the one or more organizations that are secondary for this submission.

Organization tab, selection of mutliple organizations

Variant

You have several options for describing the variant about which you wish to submit information. This section will provide more detailed hints for the Single variant cases. Entry of compound heterozygotes and haplotypes are very similar to these, just with multiple values.

Single variant, described as an HGVS expression

If you chose to describe your variant as an HGVS expression, you are required to submit the accession and version (or LRG accession) of the reference sequence, and the description of the sequence change. The tool tips provide context-specific guidance. Please consider using Mutalyzer to validate your HGVS expression before submission.

Entry of the Gene is based on current or previous official symbols from the HUGO Gene Nomenclature Committee (HGNC) .

We recommend use of the Sequence location option if you want to submit a copy number variant.

Variant tab, single variant, HGVS description

Single variant, described as sequence location

Please note carefully the assembly name and the chromosome number you want to submit, and alter the default values on the form as necessary.

For a graphical explanation of our use of inner and outer locations, please refer to dbVar's help pages .

We expect certain combinations of values for the fields defining the position of the variant. For example, a value entered for the starting position must be less than any value for a stop position. If your entry violates that rule, an error message will be displayed, and you will be directed to the section of the form that needs review.

The form uses a numbering system based on a starting value of 1, i.e. matching the numbering system you see in displays of sequence records.

clinvar submission wizard, single variant, sequence location

Conditions

The Conditions tab is used to provide the condition(s) for which the variant has been interpreted. You must first indicate whether you are interpreting a variant for a diagnostic term or a drug response. If you are not interpreting the variant for a specific disease, but you do want to indicate a set of clinical features that were observed in a patient, please select "diagnostic term", enter "See cases" as 'Database identifier for this condition or your preferred name', and then enter the clinical features on the Observations tab.

We strongly encourage use of standard identifiers to capture the concept of the condition you are describing. Note the links to those databases where you can search for the ID. Please note these hints about selecting conditions, which reference this FAQ . If you have any question, please do not hesitate to contact us.

Form used to enter condition(s) for which the variant is being interpreted

If you are submitting your interpretation of how a variant affects a drug response, the entry form is slightly different. You are asked to provide the name of the drug (preferably a term from an FDA drug label) and then the name of the condition or conditions for which the drug response is being evaluated.

image of options provided in ClinVar submission wizard when drug response is selected on the Conditions tab

If you enter more than one condition, you must clarify the relationship ("Conditions are submitted as:"). If you are providing an interpretation for multiple disorders in the same individual, please select "co-occurring". If you are submitting an interpretation about one condition or the other, but are not sure which, please select "Choice". NOTE: if you are asserting that the variant has a distinct relationship to multiple disorders independently , please submit data for each variant/condition combination as separate submissions.

This figure shows the display that results if you have clicked on Add another condition . You will note that the condition may be described either by

  • selecting a database name, and then providing the identifier from that database that most closely represents the condition you have interpreted, or
  • providing the name you prefer.

Interpretation

The form that is displayed for you to provide your interpretation depends on whether the information you submitted in the Conditions tab described a diagnostic term or drug response.

We hope these forms, with their tooltips, are self explanatory. If questions arise, more detailed instructions will be added to this section.

Observations

You can submit three types of observations as evidence for your interpretation and/or documenting the contexts in which the variant was observed and the number of occurrences. You may submit one or multiple observations of each type; there is no limit on the number. To help you keep track of your observations, we ask you to provide a label for each entry. It is in this section that you can enumerate the clinical features observed in the individuals who were assayed.

Note that all observations should be for the variant or set of variants in your submission. If you are submitting an interpretation for a single variant, your observations may include homozygotes or heterozygotes for that variant. If you are submitting an interpretation for two variants as a compound heterozygotes, then all observations should be for that combination of variants in heterozygosity (not carriers of either variant).

Please use the tool tips to guide you through your entry.

Image of the starting screen for documenting where and how often a variant was observed

Overview

The overview page gives you an opportunity to review what you have submitted, and go back to any of the sections to make changes.

NOTE: To register your submission, you MUST press one of the SUBMIT buttons on the overview page. Please do not omit this critical step.

overview tab, submission button

Support Center

Last updated: 2017-11-14T16:52:56Z