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Deletion#

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

Syntax#

Syntax sequence_identifier ":r." position "del"
Examples
  • NM_004006.3:r.123_127del
Explanation of Symbols
  • coordinate_type: the coordinate type, indicating the type of numbering used; r
  • position: the position of the nucleotide, or range of nucleotides, that is deleted; 123_127
  • 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.
  • position(s)_deleted should contain two different positions, e.g., 123_126, not 123_123.
  • the position(s)_deleted should be listed from 5' to 3', e.g., 123_126, 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 an RNA reference sequence.
  • see Uncertain; when the position and/or the sequence of a deletion has not been defined, a description may have a format like r.(100_150)delN[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: the recommendation is not to describe the variant as r.6_8deluug, i.e., describe the deleted nucleotide sequence.

    • 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).

Discussion#

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.