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Variant pages are failing if most severe consequence is not available #3624

Closed DSuveges closed 2 days ago

DSuveges commented 1 week ago

This page fails: 12_34833064_T_A

For some reason there are a handful (319) of variants where the most severe consequence id is not available, which lead to the failing of the page.

Actions:

Most likely this happens when there's no transcript:

-RECORD 0---------------------------------------
 variantId               | 12_34778206_T_C      
 chromosome              | 12                   
 position                | 34778206             
 referenceAllele         | T                    
 alternateAllele         | C                    
 inSilicoPredictors      | [{phred scaled CA... 
 mostSevereConsequenceId | null                 
 transcriptConsequences  | []                   
 rsIds                   | [rs1441442219]       
 hgvsId                  | 12:g.34778206T>C     
 alleleFrequencies       | []                   
 dbXrefs                 | [{rs1441442219, e... 
only showing top 1 row
DSuveges commented 1 week ago

Reason:

The consequence term to SO identifier mapping is defined by a dictionary in the variant index config. This dictionary doesn't contain all possible consequences.