Legend

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Diagnosis/Initial: initial diagnosis, before molecular testing

Diagnosis/Definite: phenotype individual after molecular testing

Inheritance: Indicates the inheritance of the phenotype in the family; unknown, familial (autosomal/X-linked, dominant/ recessive), paternal (Y-linked), maternal (mitochondrial), isolated (sporadic) or complex
All options:

• Unknown
• Familial
• Familial, autosomal dominant
• Familial, autosomal recessive
• Familial, X-linked
• Familial, X-linked dominant
• Familial, X-linked dominant, male sparing
• Familial, X-linked recessive
• Paternal, Y-linked
• Maternal, mitochondrial
• Isolated (sporadic)
• Di-genic
• Complex
• - = Not applicable

Age/Examination: age at which the individual was examined.

• 35y = 35 years
• 04y08m = 4 years and 8 months
• 00y00m01d12h = 1 day and 12 hours
• 18y? = around 18 years
• 30y-40y = between 30 and 40 years
• >54y = older than 54
• ? = unknown

Age/Diagnosis: age diagnosis was confirmed

Phenotype details: additional information on the phenotype of the individual, preferably use HPO terms only (http://www.human-phenotype-ontology.org/)

Age/Onset: Age first symptoms disease appeared in individual:

• 35y = 35 years
• 04y08m = 4 years and 8 months
• 00y00m01d12h = 1 day and 12 hours
• 18y? = around 18 years
• 30y-40y = between 30 and 40 years
• >54y = older than 54
• ? = unknown

Phenotype/Onset: individual's phenotype at Age/Onset described using HPO

Protein: result from protein staining

Tumor/MSI: tumor MSI (micro-sattelite instability); MSI-H (MSI-high), MSI-L (MSI-low), MSS ( microsatellite stable), ? (unknown), n/a (not analysed)

Diagnosis/Criteria: why was individual tested?

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Template: Template(s) used to detect the sequence variant; DNA (genomic DNA), RNA (cDNA) or protein
All options:

• DNA
• RNA = RNA (cDNA)
• protein
• ? = unknown

Technique: technique(s) used to identify the sequence variant.
All options:

• ? = unknown
• - = not applicable
• ARMS = amplification refractory mutation system
• 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)
• ASMM RTQ-PCR = allele-specific methylated multiplex real-time quantitative PCR
• ASO = allele-specific oligo hybridisation
• BESS = Base Excision Sequence Scanning
• CAGE = Cap analysis gene expression
• CMC = Chemical Mismatch Cleavage
• COBRA = Combined Bisulfite Restriction Analysis
• CSCE = Conformation Sensitive Capillary Electrophoresis
• CSGE = Conformation Sensitive Gel Electrophoresis
• ddF = dideoxy Fingerprinting
• DGGE = Denaturing-Gradient Gel-Electrophoresis
• DHPLC = Denaturing High-Performance Liquid Chromatography
• DOVAM = Detection Of Virtually All Mutations (SSCA variant)
• DSCA = Double-Strand DNA Conformation Analysis
• DSDI = Detection Small Deletions and Insertions
• EMC = Enzymatic Mismatch Cleavage
• expr = expression analysis
• FISH = Fluorescent In-Situ Hybridisation
• FISHf = fiberFISH
• HD = HeteroDuplex analysis
• HPLC = High-Performance Liquid Chromatography
• IEF = IsoElectric Focussing
• IHC = Immuno-Histo-Chemistry
• Invader = Invader assay
• MAPH = Multiplex Amplifiable Probe Hybridisation
• MAQ = Multiplex Amplicon Quantification
• MCA = Melting Curve Analysis, high-resolution (HRMA)
• microscope = microscope (karyotype)
• microsat = microsatellite genotyping
• minigene = expression minigene construct
• MIP = Molecular Inversion Probe amplification
• MIPsm = singele molecule Molecular Inversion Probe amplification
• MLPA = Multiplex Ligation-dependent Probe Amplification
• MLPA-ms = Multiplex Ligation-dependent Probe Amplification, methylation specific
• MS = mass spectrometry
• MSREs = Methylation sensitive restriction enzymes
• MS-SeQMA = Methylation-specific Sequence-based quantitative methylation analysis
• Ms-SNuPE = Methylation-sensitive single-nucleotide primer extension
• MyoD = myoD induced differentiation
• Northern = Northern blotting
• OM = optical mapping
• PAGE = Poly-Acrylamide Gel-Electrophoresis
• PCR = Polymerase Chain Reaction
• PCRdig = PCR + restriction enzyme digestion
• PCRlr = PCR, long-range
• PCRm = PCR, multiplex
• PCRms = PCR, methylation sensitive
• PCRq = PCR, quantitative (qPCR)
• PCRrp = PCR, repeat-primed (RP-PCR)
• PCRsqd = PCR, semi-quantitative duplex
• PE = primer extension (APEX, SNaPshot)
• PFGE = Pulsed-Field Gel-Electrophoresis (+Southern)
• PTT = Protein Truncation Test
• QMPSF = Quantitative Multiplex PCR of Short Fluorescent fragments
• RFLP = Restriction Fragment Length Polymorphisms
• RT-PCR = Reverse Transcription and PCR
• RT-PCRq = Reverse Transcription and PCR, quantitative
• SBE = Single Base Extension
• SEQ = SEQuencing (Sanger)
• SEQb = bisulfite SEQuencing
• SEQp = pyroSequencing
• SEQ-ON = next-generation sequencing - Oxford Nanopore
• SEQ-NG = next-generation sequencing
• SEQ-NG-H = next-generation sequencing - Helicos
• SEQ-NG-I = next-generation sequencing - Illumina/Solexa
• SEQ-NG-IT = next-generation sequencing - Ion Torrent
• SEQ-NG-R = next-generation sequencing - Roche/454
• SEQ-NG-S = next-generation sequencing - SOLiD
• SEQ-PB = next-generation sequencing - Pacific Biosciences
• SNPlex = SNPlex
• Southern = Southern blotting
• SSCA = Single-Strand DNA Conformation polymorphism Analysis (SSCP)
• SSCAf = fluorescent SSCA (SSCP)
• STR = Short Tandem Repeat
• TaqMan = TaqMan assay
• Western = Western Blotting

Tissue: tissue type used for analysis

Remarks: remarks regarding the screening like WGS (whole genome sequencing), WES (whole exome sequencing, gene panel (incl. a list of genes analysed), etc.

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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) (hg19): HGVS description of variant at DNA level, based on the genomic (chromosomal) DNA reference sequence; e.g. g.12345678C>T, g.12345679del, g.12345678_12345890dup

DNA change (hg38): HGVS description of variant at DNA level, based on the hg38 genomic (chromosomal) eference sequence; e.g. g.12345678C>T, g.12345679del, g.12345678_12345890dup

Published as: listed only when different from "DNA change"; variant as reported originally (e.g. 521delT). Variants seen in animal models, tested in vitro, predicted from RNA analysis, etc. are described between brackets like c.(456C>G)

ISCN: description of the variant according to ISCN nomenclature

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

Variant remarks: remarks regarding variant described, e.g. germline mosaicism in mother, 345 kb deletion, muscle RNA analysed, not in 200 control chromosomes tested, on founder haplotype, etc.

Reference: publication describing the variant submitted, incl. links to OMIM, PubMed or other source, e.g. "den Dunnen ASHG2003 P2346"

ClinVar ID: ID of variant in ClinVar database

dbSNP ID: the dbSNP ID

Origin: Origin of variant/record: Germline = in all cells, De novo = in all cells, but not in either parent, Germline/De novo (untested) = in all cells, parents not tested (use only when De novo is likely, e.g. isolated/sporadic cases with dominant disease), Somatic = present in a subset of cells, but not in either parent, Uniparental disomy = from parental disomy (maternal or paternal), CLASSIFICATION record = submitter only sharing variant classification (note another report may share Individual data), SUMMARY record = master summary record from curator (may link to another database), In vitro (cloned) = data resulting from in vitro functional assays, animal model = data from animal model, Artefact = false positive variant call, DUPLICATE record = variant already described on another chromosome (e.g. unbalanced translocation, duplicating transposition, 2nd fusion transcript, etc.)
All options:

• Germline
• De novo
• Germline/De novo (untested)
• Somatic
• Uniparental disomy
• Uniparental disomy, maternal allele
• Uniparental disomy, paternal allele
• CLASSIFICATION record
• SUMMARY record
• In vitro (cloned)
• In silico
• animal model
• Artefact
• DUPLICATE record
• Unknown
• Not applicable

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
• - = not applicable

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)

Re-site: restriction enzyme recognition site created (+) or destroyed (-); e.g. BglII+, BamHI-

VIP: variant VIP-status was requested for matchmaking - need collaboration(s) to crack the case - please contact the submitter/curator. NOTE: to get VIP status ask the curator.

Methylation: result of methylation test; GOM (gain of methylation), LOM (loss of methylation), 30% (30% methylated). NOTE: when several tests were done mention the method as well (e.g. MS-PCR 75%)

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.

Codon change: Codon change

IDbase Accession Number: IDbase Accession Number

VariO/DNA: variation ontology annotation at DNA level
All options:

• DNA substitution (VariO:0136)
• transition (VariO:0313)
• pyrimidine transition (VariO:0314)
• purine transition (VariO:0315)
• not changed (VariO:0140)
• DNA deletion (VariO:0141)
• DNA insertion (VariO:0142)
• DNA indel (VariO:0143)
• DNA inversion (VariO:0145)
• DNA translocation (VariO:0144)
• transversion (VariO:0316)
• DNA modified (VariO:0337)

VariO/Protein: variation ontology annotation at protein level
All options:

• protein truncation (VariO:0015)
• sequence retaining amino acid deletion (VariO:0016)
• nonsynonymous variation (VariO:0017)
• amino acid insertion (VariO:0018)
• amphigoric amino acid insertion (VariO:0019)
• sequence retaining amino acid insertion (VariO:0020)
• amino acid substitution (VariO:0021)
• amino acid indel (VariO:0022)
• amphigoric amino acid indel (VariO:0023)
• sequence retaining amino acid indel (VariO:0029)
• post translational modification (VariO:0028)

VariO/RNA: variation ontology annotation at RNA level
All options:

• RNA substitution (VariO:0312)
• transition (VariO:0313)
• pyrimidine transition (VariO:0314)
• purine transition (VariO:0315)
• transversion (VariO:0316)
• missense variation (VariO:0308)
• initiation codon change (VariO:0317)
• termination codon change (VariO:0309)
• nonsense variation (VariO:0310)
• silent variation (VariO:0318)
• RNA deletion (VariO:0319)
• in-frame deletion (VariO:0320)
• out-of-frame deletion (VariO:0321)
• RNA insertion (VariO:0326)
• in-frame insertion (VariO:0332)
• out-of-frame insertion (VariO:0327)
• RNA indel (VariO:0311)
• in-frame indel (VariO:0030)
• out-of-frame indel (VariO:0031)
• effect on RNA splicing (VariO:0362)
• intron gain (VariO:0364)
• variation at five prime cis splice site (VariO:0367)
• variation at canonical five prime splice site (VariO:0368)
• variation at three prime cis splice site (VariO:0370)
• variation at canonical three prime splice site (VariO:0372)
• cryptic splice site activation (VariO:0373)
• cryptic splice donor activation (VariO:0374)
• cryptic splice acceptor activation (VariO:0375)
• exon loss (VariO:0381)

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

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

Haplotype: haplotype on which variant was found

ClassClinical: classification of variant based on clinical consequences, preferably using standardised criteria; e.g. ACMG: 5, pathogenic (dominant) (= disease associated, dominant inheritance), pathogenic (recessive) (= disease associated, recessive inheritance), pathogenic (dominant, reduced risk) (= disease associated, dominant inheritance, incomplete penetrance), likely pathogenic (recessive) (= likely disease associated, recessive inheritance), 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 affects function" In ClassFunctional

Published as: listed only when different from "DNA change"; variant as reported originally (e.g. 521delT). 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

P-domain: region/domain protein affected

Exon_old: exon number according to older numbering

DNA/Legacy: original description (specify reference sequence)

Function/GVS: functional annotation of position based on the Genome Variation Server
All options:

• intergenic
• 5 flank = near gene 5
• 5'UTR
• coding
• coding near splice
• coding synonymous
• coding synonymous near splice
• codingComplex
• codingComplex near splice
• frameshift
• frameshift near splice
• missense
• missense near splice
• 5' splice
• intron
• 3' splice
• stop gained
• stop gained near splice
• stop lost
• stop lost near splice
• 3'UTR
• 3 flank = near gene 3

Effect in vitro: The effect the variant has in vitro.

Protein/Legacy: alternative description (specify reference sequence)

CodonNr: number variant codon

Method: method to screen gene
All options:

• screen APC gene (index patient)
• complete sequencing APC gene
• test known APC variant (relative)
• unknown

Predict/AGVGD: Align GVGD score; C0, C15, C25, C35, C45, C55 or C65

Predict/Grantham: Grantham score

Predict/MutationTaster: Mutation Taster prediction variant; disease causing, polymorphism

Predict/PolyPhen: PolyPhen predicted effect of variant; benign, possibly damaging, probably damaging, unknown (no prediction)

Predict/PolyPhenScore: score PolyPhen prediction (format 0.690)

Predict/SIFT: SIFT predicted effect of variant

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

FunctionalAnalysis/Result: result of functional analysis

FunctionalAnalysis/Technique: functional analysis technique(s)

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

Conservation: conservation, conservation score, (species)

CpG: Variation occurs in CpG dinucleotide; number is the position in the codon

Enzyme activity: activity variant enzym

FunctionalPrediction: predicted effect of the variant

mRNA level: Level of transcribed mRNA present in peripheral blood mononuclear cells. The level is indicated in relative terms as normal/(much) increased/(much) reduced/absent.

Predict/CADD: CADD score (Combined Annotation–Dependent Depletion) from cadd.gs.washington.edu

Predict/Splice: splice prediction

Protein/Stain: result protein staining; please indicate tissue, method used (e.g. IHC, WB, ...) and result

Protein level: Level of translated protein in peripheral blood mononuclear cells. The level is indicated in relative terms as normal/(much) increased/(much) reduced/absent.

Non_Public: non-public remarks about the entry