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Get Started with Submission to ClinVar

1. Register your organization

You must register your organization in ClinVar's Submission Portal.

2. Gather your data

What data is required to submit?

Each submission to ClinVar includes a classification of a variant for an inherited disease, cancer type, or a drug response, and the supporting evidence. More specifically, a submission includes:

  • a valid description of the variant, one of:
    • an HGVS expression
    • or chromosome coordinates and nucleotide change
  • the condition for which the variant was classified
  • the classification
  • the collection method, e.g. were the data collected from clinical testing or research
  • allele origin, e.g. germline or somatic
  • affected status of individuals with the variant

What else makes a good ClinVar submission?

Your submission will be more useful if you provide additional information, such as:

  • a comment on classification summarizing the evidence
  • the date the classification was last evaluated
  • citations relevant for the classification
  • your assertion criteria, or rules of classification
  • mode of inheritance for the variant and condition
  • number of individuals observed with the variant
  • zygosity of individuals with the variant

There is already a record in ClinVar for a variant that I intended to submit. Should I submit my data for that variant too?

Yes, you should submit your own variant classification and evidence, even if the variant is already in the database. Each additional submission adds value to the community curation of that variant by noting additional evidence and approaches to classification.

Will ClinVar change my data?

In general, ClinVar does not change data that was submitted to the database. There are a few scenarios in which we change the format, but not the content, of data during submission processing:

  • remove spaces from HGVS expressions, unless the space is between integers
  • convert HPO: to HP: and report as HP:0000000 for an HPO identifiers
  • modify "Location in gene" information according to ClinVar's conventions, including extra spaces, capitalization, abbreviations, and unsupported terms for "Location in gene"

As ClinVar evolves, there are also times when we change the format, but not the content, of data after submission processing. - These changes accommodate improvements to ClinVar's data model that are not backwards compatible. - As an example, we changed the format of some data submitted to ClinVar as functional sequence. Details of this one-time update are provided in our GitHub repository.

The only instance in which ClinVar changes the content of a submitted record is the rare case where Personal Identifiable Information (PII) was included by the submitter.

  • If PII is discovered during submission processing, NCBI staff will contact the submitter to remove the PII. No further processing of the submission will occur until the submitter removes the PII.
  • If PII is discovered after a record is published, NCBI staff will remove the PII from the submission and notify the submitter. We will also remove the PII from past releases that include the submitted record.

Can I send a test submission?

We do not have a protocol for test submissions. Instead, your first submission can be a small representative set of data that you intend to make public. You will receive feedback and additional instructions to help you put together subsequent submissions for larger datasets. You can also send any questions about submission to [email protected].

3. Choose a submission method

There are three methods for submission to ClinVar. Choose the best option for you, depending on how often you'll submit, the number of variants you'll submit, and your level of bioinformatics support.

  • Single submission wizard

    • An online form that walks you through the process of submitting a single variant classification.
    • Good for infrequent submitters who have a single variant to submit.
    • Requires no bioinformatics support.
    • Read more about using the single submission wizard.

  • File submission

    • Use one of our Excel spreadsheet templates or create tsv/csv files based on the Excel templates.
    • Most data in ClinVar are submitted using this method.
    • Good for repeat submitters and submitters with more than a few variants to submit.
    • The templates can be filled in manually or with bioinformatics support.
    • Read our instructions for file submissions.

  • Submission API

    • An API is available for submitters who want to automate the submission process.
    • Good for repeat submitters who have more than a few variants to submit and strong bioinformatics support.
    • API submissions are not reviewed by ClinVar curators. We recommend starting with a file submission before automating submissions, so that you get some initial feedback.
    • Read our instructions for submitting by API.

Once you've chosen your submission method, follow our submission instructions to prepare and submit your data.

4. Know what to expect after submission

What happens to my data after I submit it to ClinVar?

  • First, we run some automated pre-submission validation on your data.
    • You may receive some errors that need to be fixed before we can process the data.
  • Once your submission passes pre-submission validation, it goes in a queue to await review by a ClinVar curator.
    • The curator may contact you with questions to correct or clarify your submission.
    • If you are unable to get back to us with those clarifications or corrections within one month, we will delete your submission. You can resubmit the data at any time.
    • API submissions are not manually reviewed by curators, so we recommend starting with a file submission before automating submissions so that you get feedback on your approach to submission.
  • Once your submission passes curator review, it is loaded to our production server.

When will my submission be public?

  • Processing time for ClinVar submissions is typically about one week, but it can vary.
  • Turnaround time partially depends on the quality of the data in submissions and the responsiveness of submitters to questions from the curation team, so we cannot guarantee turnaround time.
  • We are unable to accommodate requests for submissions to be made public immediately, due to our submission process.
    • We recommend starting your submission early (e.g. submit to ClinVar when you submit your manuscript to the journal) and reading our submission instructions.
    • You may experience delays in processing in August, late November, and December due to holidays and vacation schedules.
  • Once your data is released, you will receive a post-submission summary from ClinVar.
    • This summary includes the accession number assigned to each of your submitted records.
    • Keep track of your accession numbers, which you will provide to ClinVar again when you update your records.

What does ClinVar do with my data once it's public?

Information about submitters

Information about variant classifications

  • All data for variant classifications are aggregated with other submissions and made public in ClinVar’s public XML files.
    • This data is freely available for any use.
    • Some data are made public but are “fuzzed” to make the information less identifiable.
      • A specific age is converted to the appropriate decade.
      • A small region submitted as "Geographic origin" may be converted to a larger region, e.g. El Salvador may be converted to Central America.
  • A subset of data is included in ClinVar’s VCF and tab-delimited summary files.
  • A subset of data is displayed on ClinVar’s website.
  • Novel variants submitted to ClinVar are also submitted to dbSNP or dbVar, as appropriate. Thus, submission to ClinVar is considered to be in compliance with NIH's Genomic Data Sharing policy.

Will ClinVar change my data?

In general, ClinVar does not change data that was submitted to the database. There are a few scenarios in which we change the format, but not the content, of data during submission processing, e.g.:

  • remove spaces from HGVS expressions, unless the space is between integers
  • convert HPO: to HP: and report as HP:0000000 for an HPO identifiers
  • modify "Location in gene" information according to ClinVar's conventions, including extra spaces, capitalization, abbreviations, and unsupported terms for "Location in gene"

The only instance in which ClinVar changes the content of a submitted record is the rare case where Personal Identifiable Information (PII) was included by the submitter.

  • If PII is discovered during submission processing, NCBI staff will contact the submitter to remove the PII. No further processing of the submission will occur until the submitter removes the PII.
  • If PII is discovered after a record is published, NCBI staff will remove the PII from the submission and notify the submitter. We will also remove the PII from past releases that include the submitted record.

Last updated: 2026-02-11T15:00:21Z