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Inversion#

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

Syntax#

Syntax sequence_identifier ":r." positions "inv"
Examples
  • NM_004006.3:r.123_345inv
Explanation of Symbols
  • coordinate_type: the coordinate type, indicating the type of numbering used; r
  • positions: the range of nucleotides that is inverted; 123_345
  • sequence_identifier: the sequence identifier used; NM_004006.3
See also explanation of grammar used in HGVS Nomenclature.

Notes#

  • all variants should be described on the DNA level; descriptions on the RNA and/or protein level may be given in addition.
  • by definition, the region inverted (positions_inverted) contains more than 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 (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 (delins) 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 frameshift.

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.

Discussion#

Is the change aagc to uucg an inversion?

No, an inversion would change aagc to gcuu, its reverse-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 reverse-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_500delins[AB053210.2:r.1289-365_1289-73inv].