Legend
Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.
Affects function: The variant's effect on the protein's function, in the format 'R/C' where R is the value reported by the source and C is the value concluded by the curator; '+' indicating the variant affects function, '+?' probably affects function, '+*' affects function, not associated with individual's disease phenotype, '#' affects function, not associated with any known disease phenotype, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect not classified.
Exon: number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = from intron 2 to intron 7, 8i_9 = intron 8/exon 9 boundary, _1 = 5' to exon 1, 18_ = 3' of exon 18, _1_18_ = encompassing the entire 18-exon gene
Exon_old: exon number according to older numbering
DNA change (cDNA): description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup
ClassClinical: Classification of the variant based on the clinical consequences as published or submitted. NOTE: this classification may differ from the opinion of the curator as given in a variant SUMMARY-record or the 'Functional effect concluded'). Classification should preferably be performed using standardised criteria; e.g. ACMG: 5 (dominant) (= disease associated, dominant inheritance), ACMG: 5 (recessive) (= disease associated, recessive inheritance), pathogenic (dominant), pathogenic (recessive), likely pathogenic (recessive) , VUS (= variant of unknown significance), likely benign (= likely not disease-associated), benign (= not disease-associated), non-disease phenotype, drug response, risk factor, associated with, etc. NOTE: pathogenic/likely pathogenic should go together with "variant (probably) affects function" In ClassFunctional
RNA change: description of variant at RNA level (following HGVS recommendations).
- r.123c>u
- r.? = unknown
- r.(?) = RNA not analysed but probably transcribed copy of DNA variant
- r.spl? = RNA not analysed but variant probably affects splicing
- r.(spl?) = RNA not analysed but variant may affect splicing
- r.0? = change expected to abolish transcription
Protein: description of variant at protein level (following HGVS recommendations).
- p.(Arg345Pro) = change predicted from DNA (RNA not analysed)
- p.Arg345Pro = change derived from RNA analysis
- p.? = unknown effect
- p.0? = probably no protein produced
Predicted: predicted consequence of variant (RNA/protein level)
All options:
- missense
- nonsense
- frameshift
- no-stop
- silent
- splicing affected
- splicing affected?
- deletion
- deletion, small
- deletion, large
- duplication
- duplication, small
- duplication, large
- insertion
- insertion, small
- insertion, large
- delins = insertion/deletion
- conversion
- other/complex
Predict/PolyPhenScore: score PolyPhen prediction (format 0.690)
Type/DNA: type of variant at DNA level. NOTE: can be derived automatically from the variant description (for all levels)
All options:
- substitution
- deletion
- deletion, small
- deletion, large
- duplication
- duplication, small
- duplication, large
- insertion
- insertion, small
- insertion, large
- delins = insertion/deletion
- inversion
- conversion
- transposition
- translocation
- other/complex
