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. 2020 Jan 8;48(D1):D835-D844.
doi: 10.1093/nar/gkz972.

ClinVar: improvements to accessing data

Melissa J Landrum  1 , Shanmuga Chitipiralla  1 , Garth R Brown  1 , Chao Chen  1 , Baoshan Gu  1 , Jennifer Hart  1 , Douglas Hoffman  1 , Wonhee Jang  1 , Kuljeet Kaur  1 , Chunlei Liu  1 , Vitaly Lyoshin  1 , Zenith Maddipatla  1 , Rama Maiti  1 , Joseph Mitchell  1 , Nuala O'Leary  1 , George R Riley  1 , Wenyao Shi  1 , George Zhou  1 , Valerie Schneider  1 , Donna Maglott  1 , J Bradley Holmes  1 , Brandi L Kattman  1
Affiliations

ClinVar: improvements to accessing data

Melissa J Landrum et al. Nucleic Acids Res. .

Abstract

ClinVar is a freely available, public archive of human genetic variants and interpretations of their relationships to diseases and other conditions, maintained at the National Institutes of Health (NIH). Submitted interpretations of variants are aggregated and made available on the ClinVar website (https://www.ncbi.nlm.nih.gov/clinvar/), and as downloadable files via FTP and through programmatic tools such as NCBI's E-utilities. The default view on the ClinVar website, the Variation page, was recently redesigned. The new layout includes several new sections that make it easier to find submitted data as well as summary data such as all diseases and citations reported for the variant. The new design also better represents more complex data such as haplotypes and genotypes, as well as variants that are in ClinVar as part of a haplotype or genotype but have no interpretation for the single variant. ClinVar's variant-centric XML had its production release in April 2019. The ClinVar website and E-utilities both have been updated to support the VCV (variation in ClinVar) accession numbers found in the variant-centric XML file. ClinVar's search engine has been fine-tuned for improved retrieval of search results.

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Figures

Figure 1.
Figure 1.
The ClinVar Variation page Summary section displays the most important aggregate data on a ClinVar VCV record.
Figure 2.
Figure 2.
The tabs on the ClinVar Variation page. (A) The Variant details tab displays general information about the variant, including submitted and calculated HGVS expressions. (B) The Conditions tab displays a summary of data aggregated by variant and condition. In this example, note that the aggregate interpretation for the variant indicates that there is a conflict. The conflict occurs between interpretations for different conditions, however, there are no conflicts in the interpretations aggregated by variant and condition. (C) The Gene(s) tab displays generation information about the gene, or genes, for the variant. In this example, the variant is located in two overlapping genes so both genes are displayed.
Figure 3.
Figure 3.
The Submitted interpretations and evidence table displays a summary of data from each submitted record for the variant. The link ‘(See all)’ in the last column header opens a configurable display (see Figure 4).
Figure 4.
Figure 4.
The Evidence details page. (A) The table displays details of each observation on each submitted record for the variant. (B) The column selector lets the submitter configure the columns the user wants to view.
Figure 5.
Figure 5.
(A) An example of a Variation ID that represents a haplotype, noted in the Description. The Variant details section lists the variants that comprise the haplotype and links to the ClinVar record for each individual variant. (B) The summary section for one of the individual variants in the haplotype. There is no interpretation for the single variant in ClinVar. Note the link ‘See interpretations for this variant in combination with other variants.’ which makes it easier to review the contexts in which this variant has been interpreted.
Figure 6.
Figure 6.
(A) Search result for a variant that has not been reported to ClinVar but is found in dbSNP. (B) Search result for a variant that is not in ClinVar, but a different variant at the same location is in the database. (C) Search result for TP53 c.619G>A, an ambiguous query for which there are two possible results.
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References

    1. Landrum M.J., Kattman B.L.. ClinVar at five years: Delivering on the promise. Hum. Mutat. 2018; 39:1623–1630. - PMC - PubMed
    1. Landrum M.J., Lee J.M., Riley G.R., Jang W., Rubinstein W.S., Church D.M., Maglott D.R.. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014; 42:D980–D985. - PMC - PubMed
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