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Examples of cases where HGVS recommendations may be confusing

1. Assigning the most 3' position possible to a deleted sequence (3' normalisation) results in discordance between a variant being described with respect to the coding sequence and the genome (chromosomal) sequence

General recommendations

  • Variants should ideally be reported in terms of the genome (chromosomal) sequence or genomic DNA sequence.
  • Variation in the genome sequence should take precedence over variation in the coding sequence.
  • Coding sequence deletions should not cross exon boundaries.

Examples

  1. Normalisation at exon boundaries when the coding sequence is antisense to the genome sequence

    • Recommended genome sequence description: NC_000017.10:g.48275364delC
    • Recommended genomic sequence description: NG_007400.1:g.8639delG
    • Recommended coding sequence description: NM_000088.3:c.590delG


  2. Several normalised variants have the same effect on the protein sequence
    • Recommended genome sequence description: NC_000007.13:g.94039133_94039135delTGT
    • Recommended genomic sequence description: NG_007405.1:g.20261_20263delTGT
    • Recommended coding sequence description: NG_007405.1(NM_000089.3):c.1035_1035+2delTGT

VariantValidator

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