Common Errors

This section lists some errors that the ClinVar API commonly returns for data.

Reference Mismatch

Message: The submitted reference allele (<BASES>) does not agree with the actual reference sequence (<BASES>)
Explanation: There is a problem with the variant that you provided.
Resolution: Fix the variant description to match the reference bases in the reference.

Message: This record is submitted as novel but it should be submitted as an update, including the SCV accession, because your organization previously submitted <SCV> for the same variant and condition.
Explanation: Your organisation has already submitted a record with this “name” and condition (OMIM code or "not provided"). ClinVar generates a variant name from your genomic coordinates. Each organisation can only have one submission for the combination of the condition and variant.
Resolution: You can either submit a revision of your interpretation, (or, e.g., extend the “observed in” information), or leave it as is. Revisions are coded by providing the ACCESSION header in the TSV file.

Message: This update changes the description of the variant for <SCV>, which is generally not allowed on a ClinVar record. Please check the description of the variant and correct if necessary. If you intend to change the description of the variant, please submit as a new record and delete this record. Contact clinvar@ncbi.nlm.nih.gov if you have questions.
Explanation: Most likely, you try to update the coordinates of a variant with an existing SCV. ClinVar does not allow this. Rather, you should remove the old variant and create a new submission.
Resolution: Remove the old variant and add a new variant instead. Note that ClinVar will store your “local variant ID”. If you resubmit a new record, make sure that this is changed or cleared such that ClinVar does not link your new request to your old submission and thinks you want to change your variant coordinates.

Message: You provided multiple diseases as the condition for the classification. If they represent related diseases along a spectrum, provide uncertain for multipleConditionExplanation. If they represent diseases that occur together in an individual with the variant (this case is rare), provide co-occurring for multipleConditionExplanation.”
Explanation: Multiple Condition IDs have been submitted for single variant. Check if this has been intentional. If multiple conditions are to be submitted, a reason needs to be included with the submission.
Resolution: Explicitly add either Uncertain, Co-occurring or Novel disease to the list of CONDITIONS.