SVD WG007

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 decribe RNA fusion transcripts

  • RNA fusion transcripts are described following the format to describe a fusion between two DNA molecules (translocations), i.e. using "::".

Examples

  • translocation fusion: NM_152263.2:r.-115_775::NM_002609.3:r.1580_*1924: a TPM3::PDGFRB fusion transcript where nucleotides r.-115 to r.775 (reference transcript NM_152263.2, TPM3 gene) are coupled to nucleotides r.1580 to r.*1924 (reference transcript NM_002609.3, PDGFRB gene)
  • deletion fusion: NM_002354.2:r.-358_555::NM_000251.2:r.212_*279: EPCAM::MSH2 fusion transcript where nucleotides r.-358 to r.555 (reference transcript NM_002354.2, EPCAM gene) are coupled to nucleotides r.212 to r.*279 (reference transcript NM_000251.2, MSH2 gene)
  • NOTES
    • ::aggcucccuugg::: a format like "::aggcucccuugg::" is used to indicate the insertion of a 12 nucletoide sequence (aggcucccuugg) between two fusion transcripts
    • NM_152263.2:r.?_775::NM_002609.3:r.1580_?: when only the break point and not the entire transcript has been analysed the format NM_152263.2:r.?_775::NM_002609.3:r.1580_? should be used

NOTE

All fusion transcripts are described using the same format irrepsective of whether they derive from inter-chromosomal or intra-chromosomal rearrangements (translocation, deletion, inversion).