SVD WG007
NOTE: We have updated our glossary and nomenclature to align with the VICC Gene Fusion Specification terminology, and clarify the distinction between chimeric transcript fusions (the biological concept) and adjoined transcripts (a nomenclature structure). The "fusion transcript" concept adopted in this consultation was relabeled to "adjoined transcript" accordingly.
Community Consultation#
Proposal SVD-WG007 (RNA fusion)#
- Status:
accepted
: proposal SVD-WG007 opened for Community Consultation on April 10 (2019), and closed June 30 (2019).
Based on the proposal the RNA Deletion-insertion page has been updated (April 2020).
The proposal suggests to extend the HGVS recommendations with a format to describe adjoined transcripts derived from gene fusions
- Adjoined transcripts are described following the format to describe a gene fusion between two DNA molecules (translocations), i.e. using "::".
Examples#
- translocation-derived adjoined transcript:
NM_152263.2:r.-115_775::NM_002609.3:r.1580_*1924
: an adjoined transcript from aTPM3::PDGFRB
gene fusion, where nucleotidesr.-115
tor.775
(reference transcript NM_152263.2, TPM3 gene) are coupled to nucleotidesr.1580
tor.*1924
(reference transcript NM_002609.3, PDGFRB gene) - deletion-derived adjoined transcript:
NM_002354.2:r.-358_555::NM_000251.2:r.212_*279
: an adjoined transcript from anEPCAM::MSH2
gene fusion, where nucleotidesr.-358
tor.555
(reference transcript NM_002354.2, EPCAM gene) are coupled to nucleotidesr.212
tor.*279
(reference transcript NM_000251.2, MSH2 gene) - NOTES
::aggcucccuugg::
: a format like::aggcucccuugg::
is used to indicate the insertion of a 12 nucleotide sequence (aggcucccuugg
) between two adjoined transcriptsNM_152263.2:r.?_775::NM_002609.3:r.1580_?
: when only the sequence adjacency and not the entire transcript has been analysed, the formatNM_152263.2:r.?_775::NM_002609.3:r.1580_?
should be used
NOTE#
All adjoined transcripts are described using the same format irrespective of whether they derive from inter-chromosomal or intra-chromosomal DNA rearrangements (translocation, deletion, inversion) or other mechanisms (trans-splicing).