RNA Recommendations

Inversion Variant


Definitions

Inversion
a sequence change where, compared to a reference sequence, more than one nucleotide replacing the original sequence are the reverse complement of the original sequence.

Description

Format: “prefix”“positions_inverted”“inv”, e.g. r.123_345inv

“prefix” = reference sequence used = r.
“positions_inverted” = range of nucleotides inverted = 123_345
“inv” = type of change is an inversion = inv


Note

  • prefix reference sequences accepted are r. (coding and non-coding RNA)
  • by definition, the region inverted (“positions_inverted”) contains more then one nucleotide. The description r.234inv is therefore not allowed; a one nucleotide inversion should be described as a substitution
  • for all descriptions the most 3’ position possible of the reference sequence is arbitrarily assigned to have been changed (3’rule)
    • the 3’rule applies to ALL descriptions (genome, gene, transcript and protein) of a given variant
  • since exon splice signals will be inverted, large genomic inversions on the RNA level usually give deletion or deletion-insertion (indel) variants
  • under discussion, see Proposal for complex variants
    { } (curly braces) can be used to list any change in the inverted sequence (“positions_inverted”) which is different when compared to the source, e.g. r.123_345inv{233a>g}
  • inversions are not used on the protein level

Examples

  • r.177_180inv
    inversion of nucleotides r.177 to r.180, changing ..aggcugauu.. to ..aggucaguu..
  • r.203_506inv
    inversion of the 304 nucleotides from position r.203 to r.506

Q&A

Is the change "aagc" to "uucg" an inversion?

No, an inversion would change "aagc" to "gcuu", its revese-complement. "uucg" is only the complement of "aagc".

Is the change "aagc" to "cgaa" an inversion?

No, an inversion would change "aagc" to "gcuu", its revese-complement. CGAA is only the reverse of "aagc".