Since references to WWW-sites are not yet acknowledged as citations, please mention den Dunnen JT and Antonarakis SE (2000). Hum.Mutat. 15:7-12 when referring to these pages.
For genomic reference sequences, nucleotide numbering is simple 1, 2, 3, ....etc. from the first to the last nucleotide of the reference seqence. No "+", "-" or other signs are used (see xxxDiscussion).
In a coding DNA reference sequence nucleotide "1" is the A of the ATG translation initiation codon. The main reason why most people prefer a coding DNA reference sequence is that from the description one immediately gets some information regarding the location of the variant;
c.78T>C > protein coding
since the nucleotide "c.78" has no signs attached and is not followed by a "+" or "-" and a second number it is located in the protein coding part of the gene. NOTE: this rules does not hold for alternative transcripts where exons might reside 5' of the translation initiation side, in an intron or 3' of the 3'-terminal exon
since the nucleotide "c.-78" has a "-" prefix it is located 5' of the ATG translation initiation codon. NOTE: the length of the 5'UTR determines whether this position is still part of the transcript or upstream of the transcription initiation site (cap site)
since the nucleotide "c.*78" has a "*" prefix it is located 3' of the translation termination codon. NOTE: the length of the 3'UTR determines whether this position is still part of the transcript or downstream of the polyA-addition site
since the nucleotide "c.78" is followed by "+" and a second number ("45") the nucleotide is in an intron, 3' of the splice donor site and before (5') of the middle of the intron
since the nucleotide "c.79" is followed by "-" and a second number ("45") the nucleotide is in an intron, 5' of the splice acceptor site and after (3') of the middle of the intron
Dividing the nucleotide number by 3 gives the number of the amino acid residue affected, in the example amino acid 26 (78:3 = 26).
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