GRCh37
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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>AClick to display gene-centric HGVS notation (Mutalyzer)

splice site information

Splice Site CoordinateRi Before Mutation Ri After Mutation Fold Change Splice TypeSite Type
470792646.39 9.036.22ACCEPTOREXONIC 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

GenersID (dbSNP150)Average Heterozygosity (dbSNP150)
SETD2Not presentNovel

cases - click to expand

allele-specific alternative splicing

likely aberrant

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 TypeCryptic Anti-Cryptic Exon Skipping Intron Inclusion Intron Inclusion with Mutation
Junction spanning9 (p=0)005 (p=0.5154)1 (p=0)
Read Abundance1.3796 (p=0.7455)0.1978 (p=0.7968)032 (p=0.3492)0

Associated IGV Screenshot

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Tissue-specific Expression Histogram

allele-specific alternative splicing

likely aberrant

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 TypeCryptic Anti-Cryptic Exon Skipping Intron Inclusion Intron Inclusion with Mutation
Junction spanning5 (p=0)002 (p=0.893)0
Read Abundance0.7593 (p=0.9261)0.1226 (p=0.9205)017 (p=0.6559)0

Associated IGV Screenshot

...

Tissue-specific Expression Histogram

allele-specific alternative splicing

likely aberrant

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 TypeCryptic Anti-Cryptic Exon Skipping Intron Inclusion Intron Inclusion with Mutation
Junction spanning8 (p=0)005 (p=0.5237)0
Read Abundance1.8889 (p=0.4919)0.3819 (p=0.474)018 (p=0.4992)0

Associated IGV Screenshot

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Tissue-specific Expression Histogram