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 affect on the protein's function, in the format Reported/Curator concluded; '+' indicating the variant affects function, '+?' probably affects function, '-' 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 = 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.

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

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: 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

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.

Gene: Here, we mention gene or locus which are reported in study. For example, if variant is intergenic, authors mapped the variants to nearby gene(s)

dbSNP ID: The dbSNP ID.

Risk allele: Risk allele are mentioned in order of their Pubmed references

Population: Population in which study has been conducted

Pubmed Reference: Links to abstracts in the PubMed database. [1] = The name of the author(s), possibly followed by the year of publication. [2] = The PubMed ID.

IGV: Reference to publication describing the variant, including links to OMIM (when available), PubMed or or other source, e.g. "den Dunnen ASHG2003 P2346".

1000G: Frequency of variant in 1000 Genomes Project

gnomAD: gnomAD

ExAC: ExAC

GTEx: Link to GTEx portal

Variant remarks: Type/kind of study that shows association of variant.

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.

Remarks: Remarks about the individual.