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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 at the DNA level, descriptions at the RNA and/or protein level may be given in addition
  • 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.
  • 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)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: 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).

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.