DNA Recommendations

Other Variant

Definitions

Chimeric
the occurrence in one individual of two or more cell populations, derived from different zygotes, with different sequences.
Mosaic
the occurrence in one individual of two or more cell populations, derived from a single zygote, with different sequences.
No change
a sequence was analysed but no variant was detected.

Description

Format: “prefix”“position(s)_analysed””=”, e.g. g.123_234=

“prefix” = reference sequence used = g.
“position(s)_analysed” = position nucleotide or range of nucleotides analysed = 123_234
”=” = not changed

Note

  • prefix reference sequences accepted are g., m., c. and n. (genomic, mitochondrial, coding DNA and non-coding DNA).
  • see SVD-WG001 (no change) for the original proposal

Examples

  • no change
    • one nucleotide
      • NC_000023.11:g.32867908=
        a screen was performed showing nucleotide g.32867908 was a “G” as in the genomic reference sequence (the nucleotide was not changed)
      • LRG_199t1:c.123=
        a screen was performed showing nucleotide c.123 was a “C” as in the coding DNA reference sequence (the nucleotide was not changed)
        NOTE: the description c.123C>C is not allowed
    • several nucleotides
      • NC_000023.11:g.32867908_32867923=
        a screen was performed showing nucleotides g.32867908 to g.32867923 were as in the genomic reference sequence (the nucleotides were not changed)
      • LRG_199t1:c.123_145=
        a screen was performed showing nucleotides c.123 to c.145 were as in the coding DNA reference sequence (the nucleotides were not changed)
      • NM_004006.2:c.[123=;456=;789=]
        a screen was performed showing nucleotides c.123, c.456 and c.789 (all on the same allele) were identical to the coding DNA reference (the nucleotides were not changed)
  • methylation
    descriptions based on Community Consultation proposal SVD-WG005
    • NC_000011.10:g.1999904_1999946|gom
      the sequence from position g.1999904 to g.1999946 showed a gain of methylation (“|gom”)
    • NC_000011.10:g.1999904_1999946|lom
      the sequence from position g.1999904 to g.1999946 showed a loss of methylation (“|lom”)
    • NC_000011.10:g.1999904_1999946|met=
      the sequence from position g.1999904 to g.1999946 showed normal methylation (“|met=”)
  • mosaicism
    • LRG_199t1:c.85=/T>C
      a mosaic case where at position 85 besides the normal sequence (a T, described as “=”) also chromosomes are found containing a C (c.85T>C)
      NOTE: irrespective of the frequency in which each nucleotide was found, the reference is always described first
  • chimerism
    • NM_004006.2:c.85=//T>C
      a chimeric case, i.e. the sample is a mix of cells containing c.85= and c.85T>C.
      NOTE: irrespective of the frequency in which each nucleotide was found, the reference is always described first