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Splicing#

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

Syntax#

Variants affecting RNA splicing result in either a deletion or insertion on the RNA level and should be described as such. Recommendations on representing adjoined transcripts formed by gene fusions are discussed in the Notes and Examples below.

Notes#

  • all variants should be described on the DNA level; descriptions on 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].
  • HGVS recommends following the HGNC guidelines and the VICC Gene Fusion Specification nomenclature to describe products of gene fusions.
    • The HGNC recommendations include using a GENESYMBOL1::GENESYMBOL2 syntax for gene-level fusion descriptions, and a GENESYMBOL1-GENESYMBOL2 syntax for read-through transcripts.
    • The VICC nomenclature extends the HGNC recommendations to include a terminology, information model, and nomenclature for gene-level and exon-level representation, with components for disambiguating regulatory fusions from chimeric transcript fusions.
    • HGVS also recommends the use of adjoined transcripts (see examples) for precise and unambiguous characterization of chimeric transcripts at the sequence level.

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 on the DNA level).

  • 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 (positions 712 / 713) is activated and the sequence from nucleotide r.650 to r.712 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.

  • 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 splice donor site, a new donor site in exon 8 (positions 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 (positions 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.

  • 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 (positions 650-51 / 650-50) and the intron 7 sequence from positions 650-50 to 650-1 is inserted in the transcript.

    • 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 (positions 831+67 / 831+68) and the intron 8 sequence from positions 831+1 to 831+67 is inserted in the transcript.

    • 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.

  • adjoined transcript (based on SVD-WG007)

    • NM_002354.2:r.-358_555::NM_000251.2:r.212_*279
      describes an adjoined transcript from an EPCAM::MSH2 gene fusion, 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 analysed, 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.

Discussion#

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 (excluding GT to GC and GC to GT variants). r.(spl?) is frequently used to indicate that 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 di-nucleotide close to the normal splice acceptor site (AG). See Uncertain.

How can I best describe the predicted consequences on 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 on the protein level".