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" |
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Examples |
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Explanation of Symbols | |
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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 asr.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 asr.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 isLRG_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.