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Deletion-Insertion (delins): a sequence change where, compared to a reference sequence, one or more nucleotides are replaced by one or more other nucleotides and which is not a substitution or inversion.


Syntax sequence_identifier ":r." position "delins" sequence
  • NM_004006.3:r.123_127delinsag
Explanation of Symbols
  • coordinate_type: the coordinate type, indicating the type of numbering used; r
  • delins: the type of change, a deletion-insertion
  • position: the position of the nucleotide, or range of nucleotides, that is deleted; 123_127
  • sequence: the RNA sequence that is inserted; ag
  • sequence_identifier: the sequence identifier used; NM_004006.3
See also explanation of grammar used in HGVS Nomenclature.


  • all variants should be described on the DNA level; descriptions on the RNA and/or protein level may be given in addition.
  • by definition, when one nucleotide is replaced by one other nucleotide, the change is a substitution.
  • two variants separated by one or more nucleotides should be described individually and not as a "delins".
    • exception: two variants separated by one nucleotide, together affecting one amino acid, should be described as a "delins" (e.g., r.142_144delinsugg p.(Arg48Trp)).
      NOTE: this prevents tools predicting the consequences of a variant to make conflicting and incorrect predictions of two different substitutions at one position.
      NOTE: the SVD-WG has prepared a proposal to modify this recommendation (see SVD-WG010). The new proposal is: two variants that are separated by fewer than two intervening nucleotides (that is, not including the variants themselves) should be described as a single "delins" variant.
  • conversions, a sequence change where a range of nucleotides are replaced by a sequence from elsewhere in the genome, are described as a "delins". The previous format "con" is no longer used (see Community Consultation SVD-WG009).
  • Adjoined transcripts from gene fusions represent a special case of deletion-insertion variant. The fusion break point is described using ::.
    NOTE: to avoid confusion, HGVS recommends to follow the HGNC guidelines to describe products of gene translocations or fusions (format GENESYMBOL1::GENESYMBOL2) and readthrough transcripts (format GENESYMBOL1-GENESYMBOL2).
  • for all descriptions, the most 3' position possible of the reference sequence is arbitrarily assigned to have been changed (3'rule).


  • r.775delinsga
    a deletion of nucleotide r.775 (a u, not described), replaced by nucleotides ga, changing ..aggcucauu.. to ..aggcgacauu...

  • r.775_777delinsc
    a deletion of nucleotides r.775 to r.777 (uca, not described), replaced by nucleotide c, changing ..aggcucauu.. to ..aggccuu...

  • r.902_909delinsuuu
    a deletion of nucleotides r.902 to r.909, replaced by nucleotides uuu.

  • r.142_144delinsugg (p.Arg48Trp)
    a deletion replacing nucleotides r.142 to r.144 (cga, not described) with ugg.
    NOTE: the variant can also be described as r.[142c>u;144a>g], i.e. two substitutions. This format is preferred when either of the two variants is known as a frequently occurring variant ("polymorphism").

  • RNA conversion (based on SVD-WG009)

    • NM_004006.2:r.2623_2803delins2804_2949
      conversion replacing nucleotides r.2623 to r.2803 (exon 21) with nucleotides r.2804 to r.2949 (exon 22) as found in the DMD coding RNA sequence file NM_004006.2.

    • r.415_1655delins[AC096506.5:g.409_1649]
      conversion replacing nucleotides r.414 to r.1655 with nucleotides g.409 to g.1649 as found in the genomic reference sequence AC096506.5.

    • r.1401_1446delins[NR_002570.3:r.1513_1558]
      conversion in exon 9 of the CYP2D6 gene, replacing exon 9 nucleotides r.1401 to r.1446 with those of the 3' flanking CYP2D7P1 gene, nucleotides r.1513 to r.1558.

  • Adjoined transcripts from gene fusions (based on SVD-WG007).

    • translocation-derived adjoined transcript
      NM_152263.2:r.-115_775::NM_002609.3:r.1580_*1924 describes an adjoined transcript from a TPM3::PDGFRB gene fusion, where nucleotides r.-115 to r.775 (reference transcript NM_152263.2, TPM3 gene) are coupled to nucleotides r.1580 to r.*1924 (reference transcript NM_002609.3, PDGFRB gene).

    • deletion-derived adjoined transcripts

      • 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 (reference transcript NM_002354.2, EPCAM gene) are coupled to nucleotides r.212 to r.*279 (reference transcript NM_000251.2, MSH2 gene).

      • NM_002354.2:r.?_555::guaugauuuuuuaataa::NM_000251.2:r.212_?
        describes an adjoined transcript from an EPCAM::MSH2 gene fusion, where only the fusion break point has been characterised, showing the insertion of a 17 nucleotide sequence (guaugauuuuuuaataa) between two adjoined transcripts.


What is an "indel"?

The term "indel" is not used in HGVS nomenclature (see Glossary). The term is confusing, having different meanings in different disciplines.

Can I describe a gc to ug variant as a di-nucleotide substitution (r.4gc>ug)?

No, this is not allowed. By definition, a substitution changes one nucleotide into one other nucleotide (see Substitution). The change augugcca to auguugca should be described as r.5_6delinsug, i.e. a deletion/insertion (delins).

The BRCA1 coding RNA reference sequence NM_007294.3 from position r.2074 to r.2080 is caugaca. A variant frequently found in the population is cauaaca (NM_007294.3:r.2077g>a). In a patient I found the sequence cauauaaca. Can I describe this variant as NM_007294.3:r.[2077g>a;2077_2078insua]?

The correct description of this variant is NM_007294.3:r.2077delinsaua.
NOTE: the answer was modified, i.e. the addition "However, since the variant is likely a combination of two other variants, it is acceptable to describe it as NM_007294.3:r.[2077g>a;2077_2078insua]." was removed.