To learn more about terms used in the database the Scientific or Plain Language.
Scientific Variant
cDNA changes in the form of ACMG standard format.
Plain Language Variant
A Variant is a change or variation in the DNA sequence of a gene and is written following a standard format or nomenclature. Variants on this website are based on the coding (c.) DNA sequence position and follow the current variant nomenclature guidelines established by the Human Genome Variation Society (HGVS). For example, c.1328G>C represents a coding DNA change at position 1328 from guanine (G) to (>) cytosine (C).
Scientific Variant ID
The ID number assigned by the database to a specific variant.
Plain Language Variant ID
The Variant ID is an identification (ID) number assigned by the database to a unique variant.
Scientific Genomic Coordinate (GRCh38)
Numbered position in the coding sequence of the reference genome where the variant starts.
Plain Language Genomic Coordinate (GRCh38)
Genomic Coordinate consists of chromosome name and integers that together define a location (position or series of nucleotides) within a reference genome. The information specified typically includes chromosome name, start position, end position, and chromosome strand.
Scientific Variant Start Position
Numbered position in the coding sequence of the gene where the variant starts.
Plain Language Variant Start Position
The Variant Start Position is the first numbered position in the DNA coding sequence of the gene where the variant starts.
Scientific Location
Region of the gene or surrounding sequence where the variant starts.
Plain Language Location
The Location is the region of the gene or surrounding sequence where the variant starts.
Scientific Amino Acid Change
Amino acid change associated with the cDNA change in standard ACMG format.
Plain Language Amino Acid Change
Gene variants may change the amino acid sequence of a protein. The predicted change that a variant may cause to the amino acid sequence of the protein is written following a standard format. For example, Arg stands for the amino acid Arginine. The Amino Acid Change is shown as the expected protein (p.) amino acid (Arg) at a numerical position (443) followed by the amino acid encoded by the change (Pro). For example, p.Arg443Pro represents a change from Arginine at position 443 to Proline.
Scientific ACMG Call
Interpretation of the variant in ACMG format (e.g. pathogenic, likely pathogenic, variant of uncertain significance/VUS) as reported by the clinical testing laboratory.
Plain Language ACMG Call
Gene variants are classified according to the likelihood of causing disease and follow guidelines from the American College of Medical Genetics and Genomics (ACMG). In this database, variants with an ACMG Call are provided by a CLIA-certified laboratory. This database focuses on variants in the following categories: variants with significant evidence to be associated with disease (pathogenic, P), variants with evidence likely to be disease causing (likely pathogenic, LP), or variants that are rare and may have some disease association evidence but still lack enough evidence to be associated with disease (variants of uncertain significance, VUS).
Scientific Last Revised Date
Date the variant was submitted or date of the last update to the variant classification provided to the website.
Plain Language Last Revised Date
The Last Revised Date is either the date the variant was first submitted or the date of last update to the variant classification provided to the website.
Scientific Predicted ACMG Call
Interpretation of the variant as reported in the literature or by use of computational programs.
Plain Language Predicted ACMG Call
A Predicted ACMG Call is provided for variants as reported in published medical literature or by use of computational methods but have not yet, as of a last revised date, been reported and/or reviewed by a CLIA certified laboratory and submitted to this database with associated evidence.
Scientific Protein Effect
Effect type can be: Deletion, Untranslated region, Frameshift, Missense, Nonsense, Synonymous/Silent, Splice donor, Splice acceptor, Duplication, Intronic, Insertion, and Deletion/Insertion.
Plain Language Protein Effect
The change or ‘effect’ that a gene variant has on a protein is reported according to the Effect Type. This includes: Deletion: parts of the DNA are missing; Untranslated region: a change in the part of the gene that controls “gene expression” (how the RNA is made from DNA or how the RNA is processed) but does not occur in the part of the DNA that describes which amino acids to place in the protein; Frameshift: amino acids are represented by three DNA/RNA sequences that represent 64 codons. The protein sequence is described by the RNA message and is “read” three nucleotide “codons” at a time whereby one of about 64 possible codons represents 20 amino acids. There are synonym codons for amino acids: this results in more codons than the number of amino acids. For example, there are 4 codons that describe the amino acid Proline (Pro). If there is an insertion or deletion in the DNA, this “frame” of three nucleotides is disrupted or shifted (frameshift) and can result in the protein terminating early and/or can result in different/incorrect amino acids being encoded; Missense: a change in DNA that changes which amino acid is used in the protein at one position; Nonsense: an early signal to stop making the protein due to a change in the DNA which changes an amino acid codon to a stop codon; Synonymous/Silent: a change in the DNA which results in a new codon but the codon still calls for the same amino acid to be placed in the same position. These changes, even though they do not affect the amino acid sequence sometimes can in fact affect splicing (how an RNA is assembled to create the final message that is translated from RNA to protein). Depending on where this change occurs, a silent change with respect to which amino acid is coded may be shown to affect how RNA is made; Splice donor or Splice acceptor: a change in the DNA that affects how RNA is trimmed to make the final protein coding message; Duplication: a part of the DNA is repeated; Intronic: a change in the DNA that does not code for amino acids but may affect how RNA is made and therefore how protein is made; Insertion: new DNA sequence added; and Deletion/Insertion: parts of the DNA is missing and a new sequence is added.
Scientific Variant Type
Gene variants are described according to the Variant Type, which include: CNV, copy number variant which here describes a change 100 DNA nucleotides or larger; SNV, single DNA nucleotide variant; small insertion; splicing, affects how RNA is made; small deletion; and small duplication.
Plain Language Variant Type
Gene variants are described according to the Variant Type, which include: CNV, copy number variant which here describes a change 100 DNA nucleotides or larger; SNV, single DNA nucleotide variant; small insertion; splicing, affects how RNA is made; small deletion; and small duplication.
Scientific PMID
The PMID references abstracts for a published article associated with the variant.
Plain Language PMID
The PubMed ID or PMID is the unique identifier number used in PubMed which is a free search engine of references on life sciences and biomedical topics and is maintained by the National Center for Biotechnology Information (NCBI). The PMID references abstracts for a published article associated with the variant.
Scientific Article Count
The number of PubMed articles associated with the variant.
Plain Language Article Count
The Article Count is the number of PubMed articles associated with the variant.
Scientific Times Observed
The number of times a variant has been observed in patients. To protect privacy, individual patient counts are not provided.
Plain Language Times Observed
The number of times a variant has been observed in patients is referenced here as Times Observed. To protect privacy, individual patient counts are not provided.
Scientific Clinical and Biochemical Phenotype
The clinical and biochemical signs and symptoms (phenotypes) reported for all patients with the variant. To protect privacy, individual patient information is not provided.
Plain Language Clinical and Biochemical Phenotype
The clinical and biochemical signs and symptoms reported for all patients with the variant are referred to as Clinical and Biochemical Phenotype. To protect privacy, individual patient information is not provided.
Scientific Display ACMG Call
In instances when a Variant has both a laboratory-provided ACMG Call and a Predicted ACMG call, the ACMG Call will be prioritized on the Variant List. Both classifications will be shown on the detailed variant page.
Plain Language Display ACMG Call
A Variant may have an ACMG Call assigned by a laboratory (refer to ACMG Call) as well as predicted from published literature (refer to Predicted ACMG Call). When both are present, this database will prioritize the ACMG Call assigned by the laboratory, referred to as Display ACMG Call.
Scientific Variants Seen With
Genotype combinations observed in the database are reported for each Variant.
Plain Language Variants Seen With
A person may have two or more variants in the same gene. For each Variant, the Variants Seen With section will list Variants seen in combination together in the database.
Scientific Disease Subtype
The type, subtype, or form of the indication associated with the specific gene Variant.
Plain Language Disease Subtype
Some conditions in this database may have different forms or types. The condition type is listed as the Disease Subtype.
Scientific Protein Domain
The distinct functional and/or structural units in the protein where the Variant occurs.
Plain Language Protein Domain
Different regions of a protein may have distinct functions or structures (called domains) that contribute to the overall job of the protein. Variants may be located in a region where they impact a specific domain of a protein (Protein Domain).
Variants
Variants
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