RNA Recommendations

Splicing Variant

Definitions

Splicing: a sequence change where, compared to a reference sequence, the normal RNA splicing pattern is altered.

Description

Variants affecting RNA splicing result in either a deletion or insertion on the RNA level and should be described as such.

Note

all variants should be described at the DNA level, descriptions at the RNA and/or protein level may be given in addition
a “,” (comma) is used to separate different transcripts/proteins derived from one allele; r.[123a>u,122_154del]

Examples

one variant, several transcripts
- NC_000023.11(NM_004006.2):r.[897u>g,832_960del]
  
  two different transcripts, r.897u>g and r.832_960del, derive from one variant (c.897T>G at the DNA level)
  
  alternative description LRG_199t1:r.[897u>g,832_960del]
splice acceptor site
- NC_000023.11(NM_004006.2):r.650_831del
  
  as a consequence of a variant destroying a splice acceptor site, the sequence from nucleotide r.650 to r.831 (exon 8) is deleted from the transcript
- NC_000023.11(NM_004006.2):r.650_712del
  
  as a consequence of a variant destroying a splice acceptor site, a new acceptor site in exon 8 (position 712 / 713) is activated and the sequence from nucleotide r.650 to r.712 is is deleted from the transcript
- NC_000023.11(NM_004006.2):r.649_650ins[650-52_650-2;c]
  
  as a consequence of a variant destroying a splice acceptor site (c.650-1G>C), a new acceptor site in intron 7 is activated and the intron 7 sequence from positions 650-52 to 650-1 is inserted in the transcript (NOTE: nucleotide 650-1 changed from g to c)
  
  alternative description LRG_199t1:r.649_650ins[650-52_650-2;c]
splice donor site (c.831+2T>A)
- NC_000023.11(NM_004006.2):r.650_831del
  
  as a consequence of a variant destroying the exon 8 splice donor site, the sequence from nucleotide r.650 to r.831 (exon 8) is deleted from the transcript
- NC_000023.11(NM_004006.2):r.778_831del
  
  as a consequence of a variant destroying the exon 8 donor acceptor site, a new donor site in exon 8 (position 777 / 778) is activated and the sequence from nucleotide r.778 to r.831 is deleted from the transcript
- NC_000023.11(NM_004006.2):r.831_832ins[ga;831+3_831+60]
  
  as a consequence of a variant destroying the exon 8 splice donor site, a new donor site in intron 8 (position 831+60 / 831+61) is activated and the intron 8 sequence from positions 831+1 to 831+60 is inserted in the transcript (NOTE: nucleotide 831+2 changed from u to a)
  
  alternative description LRG_199t1:r.831_832ins[ga;831+3_831+60]
intron variant
- NC_000023.11(NM_004006.2):r.649_650ins650-50_650-1
  
  as a consequence of an intron 7 variant (c.650-52_650-51del) a new stronger exon 8 splice acceptor site is created (position 650-51 / 650-50) and the intron 7 sequence from positions 650-50 to 650-1 is inserted in the transcript
  
  alternative description LRG_199t1:r.649_650ins650-50_650-1
- NC_000023.11(NM_004006.2):r.831_832ins831+1_831+67
  
  as a consequence of an intron 8 variant (c.831+71C>A) a new stronger exon 8 splice donor site is created (position 831+67 / 831+68) and the intron 8 sequence from positions 831+1 to 831+67 is inserted in the transcript
  
  alternative description LRG_199t1:r.831_832ins831+1_831+67
- NC_000023.11(NM_004006.2):r.649_650ins650-1400_650-1268
  
  as a consequence of an intron 7 variant (c.650-1401T>G) a new exon is created and its sequence (positions 650-1400 to 650-1268) is inserted in the transcript
  
  alternative description LRG_199t1:r.649_650ins650-1400_650-1268
fusion transcript (based on SVD-WG007)
- NM_002354.2:r.-358_555::NM_000251.2:r.212_*279
  
  describes an EPCAM::MSH2 fusion transcript where nucleotides r.-358 to r.555 (EPCAM gene, reference transcript NM_002354.2) are spliced to nucleotides r.212 to r.*279 (MSH2 gene, reference transcript NM_000251.2)
uncertain (RNA not analysed)
- NC_000023.11(NM_004006.2):r.(76a>c)
  
  RNA was not anaysed but a substitution of the “a” nucleotide at r.76 by a “c” is predicted
- NC_000023.11(NM_004006.2):r.?
  
  an effect on the RNA level is expected but it is not possible to give a reliable prediction of the consequences (RNA not analysed)
- NC_000023.11(NM_004006.2):r.spl
  
  RNA has not been analysed but it is very likely that splicing is affected

Q&A

A variant changes the +1 intron sequence (GT to AT). Although I did not analyse RNA, I am quite sure that normal splicing is affected. How can I best indicate this?

HGVS recommends to use the format "r.spl" to indicate that RNA was not analysed but splicing is most probably affected. In general the format is used for variants changing the +1, +2, -2 and -1 position of an intron, i.e. affecting the GT splice donor and AG splice acceptor site (excl. GT to GC and GC to GT variants). "r.(spl?)" is frequently used to indicate normal splicing might be affected as a consequence of variants in the first or last nucleotide of an exon, the +3 to +5 intron position (splice donor site) and variants generating a new AG-dinucleotide close to the normal splice acceptor site (AG). See Uncertain.

How can I best describe the predicted consequences at the protein level of a variant that most probably affects splicing?

The best format seems to use "p.?", meaning "I do not know what to expect at the protein level".