Last updated August 21, 2018 README file for ftp://ftp.ncbi.nih.gov/pub/clinvar/submission_templates This directory contains Excel templates for submission to ClinVar. This file documents updates and versions of the spreadsheets. April 23, 2020 Minor improvements were made to the instructions, to note that MONDO identifiers are now accepted for the Condition ID value. No changes were made to tabs or columns. ------------------------------------------------------------------------------------------------- Sept 26, 2019 In October 2019, we will retire versions 3.1 and 3.2 of the full submission spreadsheet template; earlier versions are already retired. Versions L1.4 and earlier of the lite submission spreadsheet template will also be retired. At that time, we will require submissions on versions 4.0 or 4.1 of the full template, or on version L1.5 of the lite template. ------------------------------------------------------------------------------------------------- April 30, 2019 Minor improvements were made to the instructions (updated the link to examples for Condition ID; updated examples for Variation IDs; improved instructions for translocation breakpoints). No changes were made to tabs or columns. ------------------------------------------------------------------------------------------------- August 21, 2018 Updated versions of the spreadsheet templates (versions 4.2 and L1.6) were released in error on 8/13/18. We reverted back to versions 4.1 and L1.5 on 8/21/18. These files have some improvements to the instructions, but no changes to tabs or columns. ------------------------------------------------------------------------------------------------- December 11, 2017 SubmissionTemplate.xlsx was updated to version 4.1. Updates include: - the SubmissionInfo tab is hidden; the information from this tab is provided in Submission Portal instead. This tab should not be filled in at all, unless the submission is dropped on ClinVar's ftp site instead of uploaded through Submission Portal. - on the Variant tab, the option "unknown" was removed from the column for Variant type. - on the Variant tab, a column for 'Comment on variant' was added. This column is required if the variant type is "complex". This comment is only for complex variants that cannot be sufficiently described with an HGVS expression or simple chromosomal coordinates. - on the Variant tab, "affects" was added as a value for 'Clinical significance'. This value is expected to be submitted rarely; it is used for variants that cause a non-disease phenotype, such as lactose intolerance. - on both the Variant and the CaseData tabs, the allowed values for 'Affected status' were documented in the instructions and in a pulldown menu. - on both the Variant and the CaseData tabs, a column for 'Testing laboratory interpretation' was added. This column is used in submissions that come from a clinician or a group that collects patient information, such as patient registries. It is used to report the interpretation that came from the testing laboratory, not from the submitter. - on both the Variant and the CaseData tabs, a column for 'Date phenotype was last evaluated' was added. This column is used in submissions that come from a clinician or a group that collects patient information, such as patient registries. This date is different from 'Date last evaluated', which refers to the date that the clinical significance of the variant was last evaluated. SubmissionTemplateLite.xlsx was updated to version L1.5. Updates include: - on the Variant tab, "affects" was added as a value for 'Clinical significance'. This value is expected to be submitted rarely; it is used for variants that cause a non-disease phenotype, such as lactose intolerance. - on the ExpEvidence tab, the allowed values for 'Affected status' were documented in the instructions and in a pulldown menu. ------------------------------------------------------------------------------------------------- April 28, 2016 In the summer of 2016, we will route all submissions through the ClinVar submission portal, rather than by email. The information provided in the SubmissionInfo tab of the spreadsheet can be provided in the submission portal instead. So any submissions processed through the submission portal use the submitter information from the portal, not from the spreadsheet. If your organization is not already registered in ClinVar's submission portal, please consider registering before your next submission: ================================================ https://submit.ncbi.nlm.nih.gov/clinvar/ ================================================ SubmissionTemplate.xlsx was updated to version 4.0. Updates include: - a new tab named Deletes was added. Use this tab if you need to delete one of your previous submissions (SCV). - a new tab named PhenotypicDetails is available for comment. The tab is not being processed at this time. It will be used to submit results of metabolic testing and more specific information about phenotypes for individuals reported on the CaseData tab. - on the SubmissionInfo tab, a column was added for the organization URL. This is for an organization's homepage, as opposed to base URL which is combined with the local ID to create a link to the organization's page for the specific variant. - on the SubmissionInfo tab, the "Study description" column was renamed to "Submission description". This column is for a free text description of the batch of variants in the spreadsheet. It is not specific to submissions from named studies with a "Study name". - on the SubmissionInfo tab, the Assembly column is now required for all submissions. - on the Variant tab, the "cis or trans" column was removed. - on the Variant tab, a column for "Secondary finding" was added. - on the CaseData tab, columns were added to provide different allele origins for the variants in a compound heterozygote. The additional columns are Compound het variant 1, Allele origin 2, and Compound het variant 2. - on the CaseData tab, columns were added for Testing laboratory and Date variant was reported. These columns are used when the submitter provides information from a clinical testing report but the submitter is not the testing laboratory, e.g. the submitter is a genetics clinic or a patient registry. - on both the Variant and CaseData tabs, a column was added for "Comment on clinical features". This column is used to provide free text that supplements structured phenotype data provided in the "Clinical features" column. SubmissionTemplateLite.xlsx was updated to version 1.6. Updates include: - a new tab named Deletes was added. Use this tab if you need to delete one of your previous submissions (SCV). - on the SubmissionInfo tab, a column was added for the organization URL. This is for an organization's general homepage, as opposed to base URL which is combined withe local ID to create a link to the organization's page for the specific variant. - on the ExpEvidence tab, columns were added for Testing laboratory and Date variant was reported. This is used when the submitter provides information from a clinical testing report but the submitter is not the testing laboratory, e.g. the submitter is a genetics clinic or a patient registry. - on the ExpEvidence tab, the "Ethnicity" column was renamed to "Population Group/Ethnicity" ------------------------------------------------------------------------------------------------- June 11, 2015 SubmissionTemplate.xlsx was updated to version 3.2. Updates include: - the "Left/right shifting" column was removed from the Variant tab. - the "PersonID" column was renamed "Individual ID" and moved from the Variant tab to the CaseData tab. - on the CaseData tab, instructions for co-occurring variants were updated to indicate that they are not limited to pathogenic co-occurring variants. - on the Variant tab, instructions for "Number of families with segregation observed" were updated to indicate that if a number is provided in this column, we will store Family history as "yes" even if it is not explicitly submitted. - on the CaseData tab, instructions for the "Condition comment" column were updated to indicate that if this comment is provided, the "Clinical features" column should also be filled in. - a column for "Secondary finding" was added to the CaseData tab. - on the Variant tab, instructions for Linking ID were updated to indicate that it should be a unique identifier within the submitting organization for identifier for the variant-condition pair. If we detect a conflict with a Linking ID from a previous submission, we will add the date to the identifier to make it unique. ------------------------------------------------------------------------------------------------- March 31, 2015 SubmissionTemplate.xlsx was updated to version 3.1. We will continue to process submissions on the version 2 and 3.0 templates until May 31, 2015. After that, we will require submissions on version 3.1. Updates include: - several columns for information about the submitting organization were added to the SubmissionInfo tab - several columns to describe structural variants were added to the Variant tab. - a column to indicate whether genomic coordinates for a variant are 0 or 1-based was added. - a column called 'Condition uncertainty' was added to the Variant tab; if multiple conditions are provided on a single row, this column is used to indicate if the conditions are co-occurring or whether the submitter knows the condition is one or the other but is uncertain which is correct. - two columns to support submission of criteria for making assertions of clinical significance were added to the Variant tab. Assertion method is a free text name for the document describing the assertion method; Assertion method citation lets the submitter provide a URL or a citation describing the criteria used to make assertions of clinical significance. - a column to provide aggregate counts for 'Number of hemizgyotes' was added to the Variant tab. - a column for Indication for testing was added to the Variant and CaseData tabs. This column is particularly useful for clinical testing labs who don't know the specific condition of the individual with the variant and only know the indication for the test request. - a column for Comment on evidence was added to the Variant and CaseData tabs. - a column for Condition comment was added to the Variant and CaseData tabs. This column can be used to provide a free text description of the condition to supplement controlled terms provided in other columns. - the column 'Number of independent individuals' has been removed. The concept of number of independent occurrences of a variant can be represented by providing 'Number of families with variant' instead. SubmissionTemplateLite.xlsx was updated to version L1.4. Updates include: - several columns for information about the submitting organization were added to the SubmissionInfo tab - the Review status column was moved from the Variant tab to the SubmissionInfo tab. - two columns to support submission of criteria for making assertions of clinical significance were added to the Variant tab. Assertion method is a free text name for the document describing the assertion method; Assertion method citation lets the submitter provide a URL or a citation describing the criteria used to make assertions of clinical significance. - 'phenotype' column headers on the Variant and ExpEvidence tabs were changed to use the term 'condition', e.g. Condition ID value. - the 'Method type' column on the ExpEvidence tab was renamed to 'Collection method'. ------------------------------------------------------------------------------------------------- August 18, 2014 SubmissionTemplate.xlsx was updated to version 2.1. The updates are: - the columns for "Germline/Somatic" and "Parental origin" were combined into a single column, "Allele origin". This column is required, and allowed values include all the values from "Germline/Somatic" and "Parental origin". - on the AggregateData tab, the column "Number of individuals with de novo variant" was removed. De novo variants can be idicated in the "Allele origin" column. If you wish to indicate that the variant was observed to be de novo in some but not all individuals, please submit the data on multiple rows, one row for each value for "Allele origin".