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.
Effect: The variant's effect on the function of the gene/protein, displayed in the format 'R/C'. R is the value reported by the source (publication, submitter) and this classification may vary between records. C is the value concluded by the curator. Note that in some database the curator uses Summary records to give details on the classification of the variant.Values used: '+' indicating the variant affects function, '+?' probably affects function, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect was not classified.
Exon: Number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = exons 3 to 7, 8i_9 = border intron 8/exon 9.
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.
Published as: Variant as originally reported (e.g. 521delT); listed only when different from "DNA change". Variants seen in animal models, tested in vitro, predicted from RNA analysis, etc. are described between brackets like c.(456C>G).
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
GVS function: The functional annotation of this position from the Genome Variation Server.
All options:
- intergenic
- near-gene-5
- utr-5
- start-lost
- coding
- non-coding-exon
- coding-near-splice
- non-coding-exon-near-splice
- coding-synonymous
- coding-synonymous-near-splice
- codingComplex
- codingComplex-near-splice
- frameshift
- frameshift-near-splice
- missense
- missense-near-splice
- splice-5
- splice
- non-coding-intron-near-splice
- intron
- splice-3
- stop-gained
- stop-gained-near-splice
- stop-lost
- stop-lost-near-splice
- utr-3
- near-gene-3
Clinical classification: Clinical classification of variant
Allele: On which allele is the variant located? Does not necessarily imply inheritance! 'Paternal' (confirmed or inferred), 'Maternal' (confirmed or inferred), 'Parent #1' or #2 for compound heterozygosity without having screened the parents, 'Unknown' for heterozygosity without having screened the parents, 'Both' for homozygozity.
DNA change (genomic) (hg38): Description of variant at DNA level, based on the genomic DNA reference sequence (following HGVS recommendations).
- g.12345678C>T
- g.12345678_12345890del
- g.12345678_12345890dup
Published as: Variant as originally reported (e.g. 521delT); listed only when different from "DNA change". Variants seen in animal models, tested in vitro, predicted from RNA analysis, etc. are described between brackets like c.(456C>G).
Reference: Reference to publication describing the variant, including links to OMIM (when available), PubMed or or other source, e.g. "den Dunnen ASHG2003 P2346".
DB-ID: Database ID of variant, grouping multiple observations of the same variant together, starting with the HGNC gene symbol, followed by an underscore (_) and a six digit number (e.g. DMD_012345). _000000 is used for variants where DNA was not analysed (change predicted from RNA analysis), variants seen in animal models or variants not seen in humans but functionally tested in vitro.
dbSNP ID: The dbSNP ID.
Frequency: Frequency in which the variant was found; e.g 5/760 chromosomes (in 5 of 760 chromosomes tested), 1/33 patients (in 1 of 33 patients analysed in study), 0.05 controls (in 5% of control cases tested).
Variant remarks: Remarks regarding the variant described, e.g. germline mosaicism in mother, 345 kb deletion, muscle RNA analysed, not in 200 control chromosomes tested, on founder haplotype, etc.
Template: Template(s) used to detect the sequence variant; DNA = genomic DNA, RNA = RNA (cDNA).
All options:
- DNA
- RNA = RNA (cDNA)
- Protein
- ? = unknown
Technique: Technique(s) used to identify the sequence variant.
All options:
- ? = Unknown
- arrayCGH = array for Comparative Genomic Hybridisation
- arraySEQ = array for resequencing
- arraySNP = array for SNP typing
- arrayCNV = array for Copy Number Variation (SNP and CNV probes)
- BESS = Base Excision Sequence Scanning
- CMC = Chemical Mismatch Cleavage
- CSCE = Conformation Sensitive Capillary Electrophoresis
- DGGE = Denaturing-Gradient Gel-Electrophoresis
- DHPLC = Denaturing High-Performance Liquid Chromatography
- DOVAM = Detection Of Virtually All Mutations (SSCA variant)
- ddF = dideoxy Fingerprinting
- DSCA = Double-Strand DNA Conformation Analysis
- EMC = Enzymatic Mismatch Cleavage
- HD = HeteroDuplex analysis
- MCA = high-resolution Melting Curve Analysis (hrMCA)
- IHC = Immuno-Histo-Chemistry
- MAPH = Multiplex Amplifiable Probe Hybridisation
- MLPA = Multiplex Ligation-dependent Probe Amplification
- SEQ-NG = Next-Generation Sequencing
- SEQ-NG-H = Next-Generation Sequencing - Helicos
- SEQ-NG-I = Next-Generation Sequencing - Illumina/Solexa
- SEQ-NG-R = Next-Generation Sequencing - Roche/454
- SEQ-NG-S = Next-Generation Sequencing - SOLiD
- Northern = Northern blotting
- PCR = Polymerase Chain Reaction
- PCRdig = PCR + restriction enzyme digestion
- PCRlr = PCR, long-range
- PCRm = PCR, multiplex
- PCRq = PCR, quantitative
- PAGE = Poly-Acrylamide Gel-Electrophoresis
- PTT = Protein Truncation Test
- PFGE = Pulsed-Field Gel-Electrophoresis (+Southern)
- RT-PCR = Reverse Transcription and PCR
- SEQ = SEQuencing
- SBE = Single Base Extension
- SSCA = Single-Strand DNA Conformation polymorphism Analysis (SSCP)
- SSCAf = SSCA, fluorescent (SSCP)
- Southern = Southern blotting
- TaqMan = TaqMan assay
- Western = Western Blotting
Reference: Reference to publication describing the individual/family, possibly giving more phenotypic details than listed in this database entry, including link to PubMed or other source, e.g. "den Dunnen ASHG2003 P2346". References in the "Country:City" format indicate that the variant was submitted directly to this database by the laboratory indicated.
Gender: The gender of the reported individual.
All options:
- ? = Unknown
- F = Female
- M = Male
- rF = Raised as female
- rM = Raised as male
Geographic origin: The geographic origin of the individual (country and/or region); Belgium = individual's origin is Belgium, (France) = reported by laboratory in France, individual's origin not sure.
Ethnic origin: The ethnic origin of the individual; e.g. African, Caucasian, gypsy, jew (Ashkenazi).
Population: Additional information on the individual's population.
Remarks: Remarks about the individual.
Microattribution: An acknowledgment to data contributor to this database.
