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 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.
Location: Location of variant at DNA level; note that the variant location can also be derived from the variant description.
All options:
- 5' gene flanking
- 5' UTR
- Exon
- Intron
- 3' UTR
- 3' gene flanking
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.
Position: Position of variant in coding DNA sequence; note that coding DNA position can also be derived from the variant description.
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
PolyPhen: Effect of variant, predicted by PolyPhen.
All options:
- benign = Benign
- possiblyDamaging = Possibly damaging
- probablyDamaging = Probably damaging
- noPrediction = No prediction
GVS function: The functional annotation of this position from the Genome Variation Server.
All options:
- intergenic
- near-gene-5
- utr-5
- coding
- coding-near-splice
- coding-synonymous
- coding-synonymous-near-splice
- codingComplex
- codingComplex-near-splice
- frameshift
- frameshift-near-splice
- missense
- missense-near-splice
- splice-5
- intron
- splice-3
- stop-gained
- stop-gained-near-splice
- stop-lost
- stop-lost-near-splice
- utr-3
- near-gene-3
Splice distance: The distance to the nearest splice site.
SIFT: SIFT Annotation
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.
Type: Type of variant at DNA level; note that the variant type can also be derived from the variant description (for all levels).
All options:
- Substitution
- Deletion
- Duplication
- Insertion
- Inversion
- Insertion/Deletion
- Translocation
- Other/Complex
DNA change (genomic) (hg19): Description of variant at DNA level, based on the genomic DNA reference sequence (following HGVS recommendations, and check/convert your input at https://www.mutalyzer.nl/).
- 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).
GERP: The Conservation score as calculated by GERP.
Segregation: Indicates whether the variant segregates with the phenotype (yes), does not segregate with the phenotype (no) or segregation is unknown (?)
All options:
- ? = Unknown
- yes = Segregates with phenotype
- no = Does not segregate with phenotype
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.
MSCV: MSCV|This MSCV ID is used to designate unique pathogenicity assessment even for the same variant but by different curators for different patients
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).
Sources: Variant Sources
Reference: Reference to publication describing the variant, including links to OMIM (when available), PubMed or or other source, e.g. "den Dunnen ASHG2003 P2346".
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.
Genetic origin: Origin of variant; unknown, germline (inherited), somatic, de novo, from parental disomy (maternal or paternal) or in vitro (cloned) when tested for functional consequences.
All options:
- Unknown
- Germline (inherited)
- Somatic
- De novo
- Uniparental disomy
- Uniparental disomy, maternal allele
- Uniparental disomy, paternal allele
- In vitro (cloned)
Variant_disease: DiseaseID (OMIM or MESH) for a variant with pathogenicity assessment
Date: Date the detection technique was performed, in YYYY-MM-DD format.
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
Tissue: Tissue type used for the detection of sequence variants.
Description: Screening Description
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.
Consanguinity: Indicates whether the parents are related (consanguineous), not related (non-consanguineous) or whether consanguinity is not known (unknown)
All options:
- ? = Unknown
- no = Non-consanguineous parents
- yes = Consanguineous parents
Age of death: The age at which the individual deceased, if known and applicable.
- 35y = 35 years
- 04y08m = 4 years and 8 months
- 18y? = around 18 years
- >54y = still alive at 55
- ? = unknown
Cause of death: The cause of the individual's death, if known and applicable.
Remarks: Remarks about the individual.
