ClinVar provides detailed instructions on submitting data. We recommend that you first review the ClinVar Submission Overview page to familiarize yourself with the submission process and submission template. The staff at ClinVar is always available to respond to any questions you may have about this information. They can be reached at email@example.com.
Below is a overview of the ClinVar submission instructions adapted by ClinGen. If you are interested in a consult with ClinGen prior to submitting to ClinVar, contact us at firstname.lastname@example.org. We can help you schedule a call with ClinGen support staff to discuss types of variant data and help you determine the best way to submit your data to ClinVar.
What Type of Data Are You Submitting?
For variant-level data, the primary unit of submission to ClinVar is a variant, a condition, and a clinical assertion (e.g. Pathogenic, Likely Pathogenic, Uncertain Significance, Likely Benign, Benign, Drug Response, etc.). Submissions may include additional data such as information about the variant, the date of the assertion, and mode of inheritance. Submission of supporting evidence in text or structured form is strongly encouraged including the number of observations of the variant in probands and any literature citations from which evidence for a clinical assertion was gathered.
Variant-level data does not include submission of specific patient phenotypes or demographic data and therefore does not require explicit consent from the patient for public data sharing. However, a summary paragraph of supporting evidence, including patient observations, may be included.
For case-level data, the primary unit of submission is an individual case, and includes the patient’s phenotypic features (or absence of phenotype), family history and test performed, along with the variants identified and their zygosity. Efforts are underway to increase efforts to obtain consent for individual-leve data sharing and to improve how this information is displayed in ClinVar.
Is IRB Approval Needed?
We recommend all potential ClinVar submitters discuss their sharing plans with their local IRB (if applicable). Depending on the type(s) of data being submitted, some IRBs may consider the project exempt, while others may require a more detailed review. Always check with your local IRB to ensure you are complying with their standards.
If your laboratory is not affiliated with an IRB (such as a commercial laboratory), Geisinger Health System may be able to serve as your IRB of record. Contact email@example.com to discuss this option.
Should Consent Be Obtained Before Submitting Data?
It is the responsibility of the submitter to determine if consent is needed for de-identified data you are submitting. ClinVar assumes you have obtained appropriate consent, where required, to submit the data. Once the data are in ClinVar, they are available for unrestricted distribution. Follow the link below to find guidance from ClinGen on submitting de-identified variant-level information to ClinVar when direct patient consent was not sought.
Prepare Your Data for ClinVar Submission
At this time, available submission formats include spreadsheet template, tsv/csv files and XML. Based on your laboratory’s dataset and sample output, you can decide on the best format of submission. If you have questions, contact ClinVar at firstname.lastname@example.org.
Please keep in mind, only some fields are required on the spreadsheet template. We encourage you to submit as much information to support your variant intepretation as possible. At a minimum, the following is required by ClinVar:
- 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
Submit Your Data Using the ClinVar Submission Portal
Go to the ClinVar Submission Portal:
- Register your organization first.
- You will be notified by email when your organization is approved by NCBI staff.
- Then you can send submissions to ClinVar in the Submission Portal.
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.