Nomenclature Recommendations

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

Varnomen Recommendation