Table 1 Examples of HGVS or common HGVS-like variant descriptions

From: AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature

HGVS(-like) variant descriptions (alternatives describing same genetic event)

Explanation of HGVS variant description

Disease caused by variant (cited PMIDs’ full-text uses all variant notations shown in left column)

NM_175073.2 593C>T (NP_778243.1 p.A198V)

DNA single-nucleotide substitution. Reference C replaced by alternative T at position 593 in the transcript NM_175073.2

Cerebellar ataxia with oculomotor apraxia type 1 (14506070, 16159533)

NM_006005.3 460+1G→A (NM_006005.3 IVS4+1G>A)

Splicing variant. Reference G replaced by alternative A at the genomic position 1 base pairs downstream of the 3′ end of the exon of transcript NM_006005.3 that ends at position 460

Wolfram syndrome (11317350, 12955714)

NP_000518.1 p.Asp221Thrfs*44 (NM_000527.4 c.660delC; NP_000518.1 p.Pro220Profsx45)

Protein frameshift variant. Reference aspartic acid at residue number 221 in transcript NP_000518.1 impacted by an indel resulting in an alternative threonine, with the rest of the protein being frameshifted, introducing a stop codon 44 amino acid residues downstream of residue number 221

Familial hypercholesterolemia (17539906, 22883975)

  1. Each row contains examples of a disease-causing variant description in HGVS or a common HGVS-like notation. Each of these variant descriptions describes a single genetic event causing a disease, usually by giving at least the position of the change in the gene’s transcript, an optional reference sequence, and a novel alternative (mutated) sequence. All given variants can be described using multiple commonly used notations. Examples of alternatives to the notations are shown in the left-hand column. Transcript identifiers for variant descriptions, which greatly ease the mapping of variants to reference genome positions, are often omitted by article authors and must therefore be inferred by automated methods like AVADA. The more papers that are written fully adhering to HGVS guidelines, the easier this task will become.
  2. AVADA Automatic Variant Evidence Database, HGVS Human Genome Variation Society, PMID PubMed ID.
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