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)
  • inverted duplications are described as an insertion using the format r.234_235ins123_234inv, not as r.123_456dupinv
  • since exon splice signals will be inverted, large genomic inversions on the RNA level usually give deletion or deletion-insertion (indel) variants
  • inversions are not used on protein level. Depending on the (predicted) consequences of an inversion on protein level, changes are usually described as either a delins or a frame shift.

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".

On the old nomenclature website (bottom) you had the example r.124_500delinsoAB053210.2:r.1289-365_1289-73, i.e. the "o" indicating the inserted sequence AB053210.2:r.1289-365_1289-73 was from the opposite transcriptional strand. Is the "o" still used?

No, the "o" is not used, the insertion is in an inverted orientation so "inv" should be used; r.124_500delinsAB053210.2:r.1289-365_1289-73inv.