a sequence change where, compared to a reference sequence, one nucleotide is replaced by one other nucleotide.
Format: “prefix”“position_substituted”“reference_nucleotide””>”new_nucleotide”, e.g. r.123a>g
“prefix” = reference sequence used = r. “position_substituted” = position nucleotide sustituted = 123 “reference_nulceotide” = nucleotide at reference position = a ”>” = type of change is a substitution = > “new_nucleotide” = substituted nucleotide = g
prefix reference sequences accepted are r. (coding and non-coding RNA).
the description r.76_77delinsuu is preferred over r.[76a>u;77g>u]. NOTE: by definition this change can not be described as a substitution (like r.76_77ag>uu or r.76ag>uu)
it is not correct to describe “polymorphisms” as r.76a/g (see Discussions).
a substitution of the “a” nucleotide at r.76 with a “c”
a “g” to “c” substitution 14 nucleotides 5’ of the ATG translation initiation codon
a “u” to “a” substitution 46 nucleotides 3’ of the translation termination codon
no RNA from the variant allele could be detected
RNA has not been analysed but it is very likely that splicing is affected
an effect on the RNA level is expected but it is not possible to give a reliable prediction of the consequences (RNA not analysed)
the description r.76_77delinsuu is preferred over r.[76a>u;77g>u] NOTE: based on the definition of a substitution, i.e. one nucleotide replaced by one other nucleotide, this change can not be described as a substitution like r.76_77ag>uu or r.76ag>uu
Are polymorphisms described like r.76a/g?
No, all substitutions are described as r.76a>g. In the past, the format r.76a/g has been used to describe "polymorphic" sequence variants. Note that a description should be neutral, simply describe the change, and not include any other information like predicted or known functional consequences.
Can I describe a GC to TG variant as a dinucleotide substitution (r.4gc>ug)?
No, this is not allowed. By definition a substitution changes one nucleotide into one other nucleotide. The change "ugugcca" to "uguugca" should be described as a deletion/insertion (indel) as r.4_5delinsug.