Submission to ClinVar

Do you already know how to submit to ClinVar? Go directly to the ClinVar Submission Portal.

Your organization must be registered in Submission Portal before you can submit your variant data; ClinVar does not accept submissions through email.  Read how to register in Submission Portal

Know before you submit

Can I submit to ClinVar?

ClinVar welcomes submissions from:

ClinVar assumes you have obtained appropriate consent to submit the data. Once the data are in ClinVar, they are available for unrestricted distribution.

What data can I submit?

You can submit your interpretations of variants.

  • You must submit an interpretation of either the clinical or functional significance of each variant relative to a condition.
  • ClinVar does not accept:
    • Large sets of uncurated variants from GWAS studies. Submit these data to dbGaP.
    • Variants that were observed in a patient but not interpreted for their clinical significance. Submit these data to dbSNP or dbVar, as appropriate.
    • Variants with classifications based solely on computational predictions. Variants that are classified as benign based on allele frequency, as part of a comprehensive review process, are acceptable.
  • A small number of fields are required.

The interpretation should be variant-level, not a case-level interpretation.

  • Submissions to Clinvar are considered "variant-level", because they are focused on the variant or set of variants that were interpreted.
  • You may also submit the supporting evidence for your interpretation. Evidence may be:
    • aggregate data such as reporting different data for affected individuals vs unaffected individuals
    • case data about each individual with the variant, as long as the individual is not identifiable according to NIH guidelines
  • Example -  if you have interpreted a variant that you observed in five individuals:
    • Submit your current interpretation of the variant
    • Submit your evidence as either:
      • Aggregate data for the group of five individuals with the variant
      • Case data for each of the five individuals with the variant

How many variants can I submit?

An interpretation may be for

  • a single variant
  • a set of variants that were interpreted together, as a haplotype or a compound heterozygote
    • if the variants were observed together but can be interpreted independently, please submit a separate interpretation for each variant
  • in a single submission file, you can provide one variant interpretation or thousands of variant interpretations.
  • ClinVar does not accept "individual-level" data such as an entire set of variants identified in a single individual. Please submit that data to dbGaP.

What data is required to submit?

  • submitter information including
    • the submitting organization
    • the person providing the submission
    • any people who should receive public attribution for the submission
  • a valid description of the variant, one of:
    • an HGVS expression
    • chromosome coordinates and change
    • cytogenetic description
  • the condition for which the variant was interpreted
  • an interpretation of clinical and/or functional significance
  • how the data were collected (collection method), e.g. from clinical testing or research
  • allele origin, e.g. is the interpretation for a germline or somatic variant
  • affected status, e.g. was the variant observed in affected or unaffected individuals

Your submission will be more useful to others if you also provide more supporting evidence, such as:

  • number of observations of the variant
  • mode of inheritance for the variant and condition
  • zygosity of individuals with the variant
  • presence of family history
  • ethnicity and/or geographic origin

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 clinvar@ncbi.nlm.nih.gov.

How do I get a “star” for my submission?

Submissions to ClinVar are assigned a review status, based on the type of submitter. The review status is also represented on the website by gold stars.

For a one-star submission:

For a three- or four-star submission:

How do I get accession numbers for a publication?

  • Submit early. We cannot guarantee processing time for submissions.
  • Provide your complete submission as described below.
  • Accession numbers are assigned per variant interpretation, not for the entire submission. We must have all required fields for each interpretation to assign accession numbers.
  • On the Variant tab, include a message in the “Private comment” that you need accession numbers for your publication.
  • We will give you ClinVar accession numbers for your submissions, which begin with SCV and are searchable in ClinVar.
    • You can cite these accessions in your publication.
    • Do not cite identifiers that begin with SUB or MDI; these are not searchable in ClinVar.
  • You can also provide a "submission name". You can include this name in your paper, and it can be used to search in ClinVar for the group of variants with that submission name.

If you also need your data to be held private until the paper is published:

  • in your spreadsheet, enter "hold until published"  in the column “Release status” on the SubmissionInfo tab
  • we will assign accessions for your submission, which you can include in your publication
  • we will hold your data in private until
    • you or the journal notifies us of the publication or
    • we notice the paper is published in the journal or another public database or
    • six months have passed after the time of submission; we cannot hold a submission indefinitely

To prevent a delay in the appearance of your ClinVar record, we urge submitters to contact us with the PubMed ID for the publication as soon as it is available.

You may also submit your data after publication. In this case, please include your citation in your submission.

When will my submission be public?

Processing time for ClinVar submissions varies so we cannot guarantee turnaround time. We are unable to accommodate requests for submissions to be made public immediately, due to our submission process and small staff. Therefore we recommend starting your submission early and reading our instructions for submission.

Also, you may expect delays in processing in August, late November, and December due to holidays/vacation schedules.

What does ClinVar do with my data?

Information about submitters

Information about variant interpretations

  • All data for variant interpretations is 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 Salvdor 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.

Prepare your submission

More information is available in our FAQ about submitting to ClinVar.

Spreadsheet

Two Excel spreadsheet templates are available for submissions. 

Template Use Download

Lite – SubmissionTemplateLite.xlsx

  • Minimal submissions
  • Aggregate data only
  • Variants described only with HGVS expressions
ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/submission_templates/SubmissionTemplateLite.xlsx

Full – SubmissionTemplate.xlsx

  • Minimal or detailed submissions
  • Aggregate or case data
  • Variants described with HGVS expressions, chromosome coordinates, or cytogenetic descriptions

ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/submission_templates/SubmissionTemplate.xlsx

  • To fill in the data, read our Instructions for ClinVar submission spreadsheets and the instructions in the spreadsheet itself.
  • Do not edit the names of the worksheets or columns. Our processing of the spreadsheets depends on these names.
  • Please use the most recent version of the spreadsheet to expedite processing of your submission.
    • The spreadsheet templates have version numbers on the SubmissionInfo tab.
    • Updates to the spreadsheet templates are documented in a README file on the ftp site
  • We only accept .xlsx files, not .xls or xlsm. Please save files with the latter formats as .xlsx before submitting to ClinVar.
  • Use a browser other than Safari to download the templates.
    • Safari will probably redirect you to Finder, and give you the impression that you need credentials for the ftp site.
    • You do not need login credentials to access content on ClinVar's ftp site.
    • You will not encounter this problem with Firefox or Chrome.

tsv/csv files

You can submit your data in tsv or csv files that are based on the columns in the spreadsheet templates.

  • Choose a base name for all files in your submission
  • Create a set of files, each with the same base name and corresponding to each tab in the spreadsheet
    • e.g. a submission based on SubmissionTemplateLite.xlsx has the following files:
      • FILENAME.SubmissionInfo.csv
      • FILENAME.Variant.csv
      • FILENAME.ExpEvidence.csv
    • e.g. a submission based on SubmissionTemplatel.xlsx has the following files:
      • FILENAME.SubmissionInfo.csv
      • FILENAME.Variant.csv
      • FILENAME.CaseData.csv (optional, if case data is provided as evidence)
  • Note that the file names are case-sensitive, e.g. FILENAME.Variant.csv, not FILENAME.variant.csv
  • Include the column headers exactly as in the spreadsheet in the first line of each file.
    • You only need to provide column headers for columns where you provide data.
      • e.g. if you only submit the required fields, only those columns need to be in the file
    • The order of the columns does not matter.
  • To fill in the data, read our Instructions for ClinVar submission spreadsheets and the instructions in the spreadsheet itself.

XML

Detail-rich submissions are more readily submitted by XML.

Submission wizard

If you have one variant interpretation to submit and would rather not fill out the spreadsheet, you can use the ClinVar single submission wizard in the Submission Portal. This wizard guides you through submission of a single interpretation at a time, prompting you to describe the variant, the condition, your interpretation, and the supporting evidence. See the help documentation for the ClinVar submission wizard and our YouTube video.

Send your submission

  1. Review the documentation and spreadsheet templates on the ftp site. If you have any questions, send them to clinvar@ncbi.nlm.nih.gov.
  2. Go to the ClinVar Submission Portal.
    1. Register your organization first.
    2. You will be notified by email when your organization is approved by NCBI staff.
    3. Then you can send submissions to ClinVar in the Submission Portal.
  3. There are two options in Submission Portal:
    • If you are using one of the file formats described above, use the "Upload new file submission button" to upload your file(s).
    • If you are using the ClinVar single submission wizard, use the "ClinVar single submission wizard" button to enter your data online.
  4. If you have any problems using the Submission Portal, please contact us at clinvar@ncbi.nlm.nih.gov so that we can help you with the process.

Update your submission

When can I update?

You can update your submissions to ClinVar at any time. For example, you may want to update because:

  • you have reclassified the variant
  • you have determined the condition to associate with the variant
  • you have more observations of the variant to describe
  • you submit for a clinical testing laboratory and you want to send regular submissions, including both new submissions and updates, so that your laboratory's classifications do not become outdated in ClinVar.

What information can I update?

Any data point in a ClinVar submission may be updated.

  • If you are updating the description of the variant because it was incorrect, the submission is assigned a new SCV accession number.
  • If you are updating any other type of data, the submission retains the same SCV accession number.
  • You may also merge together two redundant submissions or delete submissions, if necessary.

How do I make the update?

You can submit an update with the spreadsheet template:

  1. provide all information for the variant interpretation, including the updated information
    • the update overwrites your previous submission, rather than adding to it, so include all previous information that you want to retain
  2. on the Variant tab
    • include the SCV accession number for your submission in the "ClinVarAccession" column
    • enter "update" in the "Novel or update" column
  3. submit your spreadsheet as described above

The ClinVar single submission wizard does not accept updates yet, but it will in the future.

Last updated: 2017-09-21T16:05:52-04:00