NCBI releases newly designed dbSNP RefSNP Report – Alpha version


NCBI dbSNP is pleased to announce a newly designed Reference SNP (RefSNP, rs) Report webpage to provide enhanced performance and presentation for access to individual RefSNP records. This Alpha version of the report enables browsing of submitted and computed RefSNP variant data from the redesigned dbSNP build system.

The new RefSNP report (alpha version). You can see all of the sections described in the blog post, like the summary section and the sidebar menu.

Figure 1. The dbSNP RefSNP Report Alpha for rs268.

Highlights of the RefSNP Report – Alpha:

  • A summary section at the top of the page provides a snapshot view of the variant by highlighting important details such as: Organism, Position, Alleles, Variation Type, Frequency, Clinical Significance, Gene and Consequence, Publications, and a Genomic View to explore the variant in the context of the genome.
  • The sidebar menu allows fast and easy access to the following RefSNP details:
    1. Variant Details include data related to known variant placements on genomic sequences as well as on transcript and protein sequences.
    2. Clinical Significance reports entries from ClinVar associated with the variant, per each allele.
    3. Frequency displays a table of minor allele frequencies (MAF) as reported by 1000 Genomes.
    4. Aliases includes all known HGVS representations of variant placements and allele changes, on genomic and non-genomic sequences.
    5. Submissions provides a list of the original Submitters of variations collected in support of a given RefSNP cluster, along with Submission type (SubSNP, Genotype, ClinVar), Submission identifier along with Date and the Build number.
    6. History lists other RefSNP identifiers from previous builds (Build column) that now support the current RefSNP.
    7. Publications lists all PubMed articles citing a given rs variation.
  • Genomic regions, transcripts, and products allows exploration of the genomic context for a given RefSNP in the NCBI Sequence Viewer. This section also allows an easy option to launch and view the RefSNP and neighboring variants in the NCBI Variation Viewer.

How to access the newly designed RefSNP Report Alpha?

RefSNP Report Alpha can be accessed by clicking on the banner on the top right of the current dbSNP report page (see image below) or directly by using the following URL as an example: https://www.ncbi.nlm.nih.gov/snp/rs268. The link works for any rs known in the current system. The new report page will remain available in parallel with the existing dbSNP RefSNP report.

The banner at the top right of the current dbSNP report page reads

Figure 2. The banner at the top right of the dbSNP report page (outlined in red) links to RefSNP Report Alpha.

Feedback

We would love to know your thoughts on the new RefSNP Report Alpha. Please use the ‘FEEDBACK’ button on the left margin of the page to share your opinions.

The feedback button is on the left side of the RefSNP report page

Figure 3. Click the Feedback button (outlined in red) to tell us what you think about the new RefSNP report.

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