RNA Recommendations

Deletion Variant

Definitions

Deletion
a sequence change where, compared to a reference sequence, one or more nucleotides are not present (deleted).

Description

Format: “prefix”“position(s)_deleted”“del”, e.g. r.123_127del

“prefix” = reference sequence used = r.
“position(s)_deleted” = position nucleotide or range of nucleotides deleted = 123_127
“del” = type of change is a deletion = del 1

Note

  • all variants should be described at the DNA level, descriptions at the RNA and/or protein level may be given in addition
  • prefix reference sequences accepted are r. (coding and non-coding RNA).
  • the “position(s)_deleted” should contain two different positions, e.g. 123_126 but not 123_123.
  • the “position(s)_deleted” should be listed from 5’ to 3’, e.g. 123_126 but not 126_123.
  • for all descriptions the most 3’ position possible of the reference sequence is arbitrarily assigned to have been changed (3’rule)
    • the 3’rule also applies for changes in single residue stretches and tandem repeats (nucleotide or amino acid)
      NOTE: the exception to the 3’rule for deletions around exon/exon junctions see Deletions does not apply when describing variants based on a RNA reference sequence
  • 1 = see Uncertain; when the postion and/or the sequence of a deletion has not been defined, a description may have a format like r.(100_150)del(15)

Examples

  • one nucleotide
    • LRG_199t1:r.10del
      a deletion of the U at position r.10 in the reference sequence LRG_199t1
  • several nucleotides
    • NM_004006.2:r.6_8del
      a deletion of nucleotides r.6 to r.8 in the reference sequence NM_004006.2
      NOTE: it is allowed to describe the variant as r.6_8deluug
    • LRG_2t1:r.1034_1036del
      a deletion of nucleotides r.1034 to r.1036 (“uug”) in the reference sequence LRG_2t1
      NOTE: since the 3’rule has to be applied the variant, crossing the intron between nucleotides r.1035 and r.1036, is not described as r.1033_1035del (deletion “guu”)
    • LRG_199t1:r.(4072_5145del)
      the predicted deletion of exon 30 (starting at position r.4072) to exon 36 (ending at position r.5145) of the DMD-gene; RNA has not been analysed
  • LRG_199t1:r.=/6_8del
    a mosaic case where from position r.6 to r.8 besides the normal sequence also transcripts are found containing a deletion of this sequence
    NOTE: for the predicted consequences of a variant the description is LRG_199t1:r.(=/6_8del)

Q&A

Can I use r.123del6 to describe a 6 nucleotide deletion?

No, a deletion of more than one residue should mention the first and last residue deleted, separated using the range symbol ("_", underscore), e.g. r.123_128del and not r.123del6.

Is the description of a deletion of exon 17 as r.EX17del still allowed?

A description like r.EX17del has never been allowed. Descriptions should be specific and indicate the nucleotides affected by the change.