Veridical validated this mutation based on 19 reads which span the splice junction and extend into the intron.
Veridical validated this mutation based on 19 reads which span the splice junction, extend into the intron, and contain the mutation in question.
Veridical validated this mutation based on 596 reads each of which either overlap the splice boundary or are wholly contained within an intron.
Evidence Type
Cryptic
Anti-Cryptic
Exon Skipping
Intron Inclusion
Intron Inclusion with Mutation
Junction spanning
0
0
0
19 (p=0.0027)
19 (p=0)
Read Abundance
0.5 (p=0.8255)
0.2185 (p=0)
0
596 (p=0)
0
Associated IGV Screenshot
Tissue-specific Expression Histogram
Overview
Each case in the ValidSpliceMut database is classified as
aberrant, likely aberrant, or allele-specific alternative splicing based on a series of evidence types. Steps taken to classify cases are presented in the flowchart below. After a classification has been determined for all cases containing the specified variant in ValidSpliceMut (regardless of tumour type), the most common classification - labelled "Consensus molecular phenotype" - is shown at the top of the results page. Adjacent to the consensus molecular phenotype, the number of cases assigned the most common classification is displayed alongside the total number of cases. Multiple classifications are listed if multiple classifications are equally common.
Classification Flowchart
Flowchart depicting steps taken to classify the molecular phenotype of cases. Click the flowchart to view an enlarged version in a new tab, or click one of the buttons below to view the flowchart in a specified file format.
Although cases are classified according to three distinct classifications, there are of course many combinations of evidence types which can lead to a classification (as depicted in the flowchart above). During case classification, all evidence types are calculated first, then a series of rules are applied to arrive at a single classification. The classification evidence bar is constructed using a point-based system which takes into account all evidence types relevant to the site type (NATURAL/CRYPTIC). The position of the bar within a single classification region reflects the balance between evidence supporting and contrasting the assigned classification. Supporting evidence moves the bar to the right, while contrasting evidence moves the bar to the left. If an equal amount of supporting and contrasting evidence types are present, the bar will appear directly in the middle of the region. The classification assigned to a case is made larger, bolded, and underlined. A classification evidence bar is present in the dropdown area for each case.
Example classification evidence bar
allele-specific alt splicing
likely aberrant
aberrant
Additional Reclassification
Cases presented on ValidSpliceMut are grouped by variant, splice type (DONOR/ACCEPTOR), and site type (NATURAL/CRYPTIC). Cases are assigned a classification based on the effect of a variant on a single splice site "in a vacuum". However, the presence of an aberrant case in another site affected by the same variant, in the same tumour type, provides additional evidence the presence of the variant may produce an aberrant molecular phenotype. Thus, when displaying the predicted molecular phenotype classification for each case, classifications of other splice sites (NATURAL vs CRYPTIC) in the same tumour type affected by the same variant are also examined. If any of these other sites are classified as aberrant, all of them are reclassified as aberrant. In the event a reclassification has occurred, it is denoted as such below the classification evidence bar associated with the case.
