ClinVar variant_summary.txt and submission_summary.txt files are currently used to obtain relevant metadata on reported variants and as input for addressing conflicting calls. Since submission_summary.txt may include multiple rows per variant with different ClinicalSignificance values, we need to ensure the correct call is retained in a manner consistent with AutoGVP's pathogenicity assessment steps with ClinVar. This can be performed as follows:
If variant_summaryClinicalSignificance == submission_summaryClinicalSignificance at last date evaluated, retain call
If variant_summaryClinicalSignificance != submission_summaryClinicalSignificance, but a submission_summary P-LP call has associated PhenotypeInfo, retain P-LP call.
If variant_summaryClinicalSignificance != submission_summaryClinicalSignificance, retain call in submission_summary at last date evaluated.
rjcorb
commented
1 year ago
Provide the command used or report the bug here
ClinVar
variant_summary.txtandsubmission_summary.txtfiles are currently used to obtain relevant metadata on reported variants and as input for addressing conflicting calls. Sincesubmission_summary.txtmay include multiple rows per variant with differentClinicalSignificancevalues, we need to ensure the correct call is retained in a manner consistent with AutoGVP's pathogenicity assessment steps with ClinVar. This can be performed as follows:variant_summaryClinicalSignificance==submission_summaryClinicalSignificanceat last date evaluated, retain callvariant_summaryClinicalSignificance!=submission_summaryClinicalSignificance, but asubmission_summaryP-LP call has associated PhenotypeInfo, retain P-LP call.variant_summaryClinicalSignificance!=submission_summaryClinicalSignificance, retain call insubmission_summaryat last date evaluated.What version are you using?
latest version
Add error message here (if applicable)
Add Session info
Run
sessionInfo()and post the output below