reference sequences accepted are g., m., c. and n. (genomic, mitochondrial, coding DNA and non-coding DNA).
repeated sequences include both small (mono-, di-, tri-, etc., nucleotide) and larger (kilobase-sized) repeats.
the format based on repeat position is preferred, descriptions of the repeat sequence quickly become too lengthy.
NOTE: while g.123CAG describes a repeat of 23 CAG units, g.123_125 describes a tri-nucleotide repeat of 23 units which could be interrupted with other units (e.g. a rare CAA). The description g.123CAG can thus only be used when the repeat was sequenced.
the format g.123_124TG, should not be used; it contains redundant information (“123_124” and “TG”).
for composite repeats the basic format can be used, successively listing each different repeat unit; g.456_465466_489490_499.
a repeated di-nucleotide sequence, with the first unit located from position g.123 to g.124, is present in 14 copies on one allele and 18 copies on the other allele
in literature the Fragile-X tri-nucleotide repeat is known as the CGG-repeat. Hoever, based on a coding DNA reference sequence (GenBank NM_002024.5) and applying the 3’rule, the repeat has to be described as a GGC-repeat see Recommendations.
an extended repeat of exactly 79 units
NOTE : c.-128GGC can only be used when the repeat has been sequenced, excluding it is interrupted by one or more GGA-triplets
the repeated tri-nucleotide sequence, starting at position c.-128, has an estimated size of between 600 to 800 copies.
NOTE: the repeat can be pure or a mix of GGC and GGA triplets.
based on the HTT (huntingtin) coding DNA reference sequence (GenBank LRG_763t1 (NM_002111.8), applying the 3’rule, the Huntington’s Disease tri-nucleotide repeat is described as an GCA (not CAG) repeat.
NOTE: the coding DNA reference sequence (LRG_763t1 (NM_002111.8)) was determined and shown to contain an allele of 21 GCA repeats
NOTE: on protein level the reference allele contains 23 Gln’s, described as p.Gln18 (alternatively p.Q18). The difference derives from the fact that the GCA repeat is interrupted by ACA-triplet (“CAA” coding) at position 20.
the coding DNA reference sequence (LRG_763t1 (NM_002111.8)) was determined and shown to contain a tri-nucleotide allele of 21 GCA, 1 ACA, 2 GCC, 1 ACC and 10 GCC-repeats.
NOTE: when the sequence was not determined, but the repeat estimated based on PCR fragment size, the description is c.(54_56;117_119;120_122;126_128;129_131)
a complex repeated sequence has a first unit located from position g.456 to g.457, present in 4 copies, a second unit from position g.466 to g.468 present in 9 copies and a third unit (mono-nucleotide) starting at position position 490 present in 12 copies.
Intron 9 of the CFTR gene ends with the sequence ...tgtgtgtgtgtttttttaacag[exon_10]. Both the TG and T stretches are variable in length (from 9 to 13 and 5 to 9 resp.). The reference sequence has 11 TG copies and 7 T's. Is it correct to describe an allele as c.1210-14TGT or for the T stretch as c.1210-6T?
A complex case. First note that by applying the 3'rule it is a variable GT and not TG stretch. When the coding DNA reference sequence has TG11 followed by T7, the reference allele is described as c.1210-33GT1210-11. When only variability of the T-stretch is reported, the reference allele is described as c.1210-12. To indicate the overall variability found in the population the description is c.1210-33GT[(9_13)]T[(4_8)] for the combined repeat and c.1210-12[(5_9)] for the T-stretch.