SVD WG011

Community Consultation#

Proposal SVD-WG011 (RNA insertions)#

Status: open

Proposal SVD-WG011 opened for Community Consultation on May 11th, 2026, closing on August 11th, 2026.
Vote and providide feedback on GitHub.

The proposal suggests to specify the HGVS nomenclature recommendations for the description of variants on the RNA level, more specifically the insertion of intron sequences. Please vote for the proposal and provide feedback on the associated GitHub discussion.

Background

As the r. prefix refers to mature (coding/non-coding) RNA molecules, descriptions using the r. prefix can not refer to intronic nucleotide positions. Therefore, variant descriptions like NC_000023.10(NM_004006.3):r.5448_5449ins5448+1_5448+66 are actually invalid. Furthermore, r.5448_5449 would not be referring to adjacent nucleotides if r. descriptions would allow intronic positions.

Proposal

  • the proposal applies to variant descriptions on the RNA level.
  • the HGVS nomenclature requires that inserted sequences derived from intron sequences using a coding/non-coding DNA reference sequence (NM_ or NR_) are described using the format ins[c.5448+1_5448+66], i.e. referencing the coding/non-coding DNA reference sequence and using the c./n. prefix.

NOTE: officially, the insertion should be described using the format ins[NC_000023.11(NM_004006.3):c.5448+1_5448+66], however, since the description at the DNA level already includes the reference sequences used (NC_000023.11 and NM_004006.3), specifying them again would mean the unnecessary use of redundant information.

Examples#

  • r.5448_5449ins[c.5448+1_5448+66]
    on RNA level, variant NC_000023.11(NM_004006.3):c.5448+67A>G gives the insertion of intronic nucleotides c.5448+1 to c.5448+66 between nucleotides r.5448 and r.5449.
    NOTE: since the HGVS nomenclature demands that variants must be described on DNA level, a full description of the variant is like NC_000023.11:g.32348339T>C   NC_000023.11(NM_004006.3):c.5448+67A>G   r.5448_5449ins[c.5448+1_5448+66].

  • r.1704_1705ins[GA;c.1704+3_1704+11]
    on RNA level, variant NC_000023.11(NM_004006.3):c.1704+2T>A gives the insertion of nucleotides GA and c.1704+3 to c.1704+11 between nucleotides r.1704 and r.1705.
    NOTE: since the HGVS nomenclature demands that variants must be described on DNA level, a full description of the variant is like NC_000023.11:g.32573743A>T   NC_000023.11(NM_004006.3):c.1704+2T>A   r.1704_1705ins[GA;c.1704+3_1704+11].
    NOTE: since nucleotide c.1704+2 changes from T to A, the insertion can not be described as r.1704_1705ins[c.1704+1_1704+11].

  • r.8668_8669ins[c.8669-68_8669-25;c.8669-18_8669-1]
    on RNA level, variant NC_000023.11(NM_004006.3):c.8669-24_8669-19del gives the insertion of nucleotides c.8669-68 to c.8669-25 and c.8669-18 to c.8669-1 between nucleotides r.8668 and r.8669.
    NOTE: since the HGVS nomenclature demands that variants must be described on DNA level, a full description of the variant is like NC_000023.11:g.31478393_31478398del   NC_000023.11(NM_004006.3):c.8669-24_8669-19del   r.8668_8669ins[c.8869-68_8869-25;c.8869-18_8869-1].
    NOTE: since nucleotides c.8669-24 to c.8669-19 are deleted, the insertion can not be described as r.8668_8669ins[c.8669-68_8669-1].

  • r.94_264delins[NC_000008.11:g.16511847_16511910inv]
    on RNA level, a DNA variant disrupts normal splicing and gives the deletion of nucleotides r.94 to r.264, being replaced with the insertion, in an inverted orientation, of nucleotides NC_000008.11:g.16511847 to g.16511910 from chromosome 8.
    NOTE: since the HGVS nomenclature demands that variants must be described on DNA level, a full description of the variant is like NC_000023.11:g.32854892_32854897delins[CCA;NC_000008.11:g.16489201_16564934]   NC_000023.11(NM_004006.3):c.94-5077_94-5072delins[NC_000008.11:g.16489201_16564934inv;TGG]   r.94_264delins[NC_000008.11:g.16511847_16511910inv].