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Consensus molecular phenotype: aberrant (3 of 3 cases)
variant position
Genomic Position (g. notation) | Gene-centric HGVS Notation (c. notation) | chr3:g.47079269T>A | Click to display gene-centric HGVS notation (Mutalyzer) |
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splice site information
Splice Site Coordinate | Ri Before Mutation | Ri After Mutation | Fold Change | Splice Type | Site Type |
---|---|---|---|---|---|
47079264 | 6.39 | 9.03 | 6.22 | ACCEPTOR | EXONIC CRYPTIC † |
† site has a lower Ri value than the nearest natural site of the same type and is therefore expected to be used less frequently
variant data
Gene | rsID (dbSNP150) | Average Heterozygosity (dbSNP150) |
---|---|---|
SETD2 | Not present | Novel |
cases - click to expand
allele-specific alternative splicing
likely aberrant
View TCGA-A3-3358 metadata (NCI Genomic Data Commons)
Veridical validated this mutation based on 9 reads, each split between the predicted cryptic site and an adjacent exon.
Veridical validated this mutation based on 1 reads which span the splice junction, extend into the intron, and contain the mutation in question.
Evidence Type | Cryptic | Anti-Cryptic | Exon Skipping | Intron Inclusion | Intron Inclusion with Mutation |
---|---|---|---|---|---|
Junction spanning | 9 (p=0) | 0 | 0 | 5 (p=0.5154) | 1 (p=0) |
Read Abundance | 1.3796 (p=0.7455) | 0.1978 (p=0.7968) | 0 | 32 (p=0.3492) | 0 |
allele-specific alternative splicing
likely aberrant
View TCGA-80-5607 metadata (NCI Genomic Data Commons)
Veridical validated this mutation based on 5 reads, each split between the predicted cryptic site and an adjacent exon.
Evidence Type | Cryptic | Anti-Cryptic | Exon Skipping | Intron Inclusion | Intron Inclusion with Mutation |
---|---|---|---|---|---|
Junction spanning | 5 (p=0) | 0 | 0 | 2 (p=0.893) | 0 |
Read Abundance | 0.7593 (p=0.9261) | 0.1226 (p=0.9205) | 0 | 17 (p=0.6559) | 0 |
allele-specific alternative splicing
likely aberrant
View TCGA-UF-A7JT metadata (NCI Genomic Data Commons)
Veridical validated this mutation based on 8 reads, each split between the predicted cryptic site and an adjacent exon.
Evidence Type | Cryptic | Anti-Cryptic | Exon Skipping | Intron Inclusion | Intron Inclusion with Mutation |
---|---|---|---|---|---|
Junction spanning | 8 (p=0) | 0 | 0 | 5 (p=0.5237) | 0 |
Read Abundance | 1.8889 (p=0.4919) | 0.3819 (p=0.474) | 0 | 18 (p=0.4992) | 0 |