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Deletion-Insertion#

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#

Syntax sequence_identifier ":r." position "delins" sequence
Examples
  • 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.

Notes#

  • 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).

Examples#

  • 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.

  • Example adjoined transcripts from gene fusions are discussed in the adjoined transcript recommendations.

Discussion#

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.