RefSNP Report Help

 

This document describes the redesigned NCBI dbSNP RefSNP Web Report. You can learn more about RefSNP here.

Send us email with feedback about any problems you may encounter to dbSNP-support@nlm.nih.gov.

RefSNP Report

dbSNP RefSNP Web Report is an interactive page for browsing the submitted and computed information for a single Reference SNP variant (RefSNP, rs).

The top of the page is the RefSNP Summary section, reporting concise information related to the variation, with more specific details included in the corresponding tabs:

  • Variant Details Variant chromosome, mRNA, and protein positions. Mapped gene information including mRNA transcripts, functional consequence annotations (missense, splice-site, etc.), and protein amino acid changes.
  • Clinical Significance
  • Frequency
  • Aliases
  • Submissions
  • History
  • Publications
  • Genomic View

RefSNP orientation

All alleles are reported in the Forward orientation.

RefSNP neighbors

Use the Genomic View link in Summary to examine the rs and its neighbors in the latest genomic context.

Printing the report

In order to print the report use Ctrl+P or the Print option inside your internet browser.  

Searching for another RefSNP Report

Use the Search box above the Summary to find and explore other RefSNP (rs) records.  

Enter the rs identifier (ie.rs268) and click "Search".

Currently the page only supports searching for exact rs identifiers, not for rs attributes.  

RefSNPreport_Search

Summary 

Summary contains the essential information about the variant in the form of tag-value pairs for Organism, Position, Alleles, Variation Type, Frequency, Clinical Significance, Gene and Consequence, Publications, and Genomic View. SNPs with LitVar information are also labeled on refsnp page, under the 'Publications' item.

RefSNPreport_Summary

Variant Details

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_).
The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed.
Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view flanking nucleotides and neighbor rs use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

RefSNPreport_VariantDetails

Clinical Significance

Clinical Significance shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 16589) to access the full ClinVar report.

RefSNPreport_ClinicalSignificance

Frequency

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. The top table display frequency from NCBI ALFA project and the table below display all projects in dbSNP including 1000Genomes, GnomAD, and TOPMED.
Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available.
Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").
The Download button allows to download the frequency table as a Tab-separated file.

RefSNPreport_Frequency

Aliases

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change.
The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

RefSNPreport_Aliases

Aliases Filter

To limit the display to a sequence type or alias of interest use the “Filter” box as shown in the example below to select only desired HGVS aliases, based on NM sequences for mRNA.

RefSNPreport_Aliases_Filter

Submissions

Submissions tab displays variations originally submitted to dbSNP, and now supporting this RefSNP cluster (rs).
We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time.
Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

RefSNPreport_Submissions

Submissions Filter

The list of submitters can be long, so use the "Filter" box to find a given submitter (1000 Genomes).

RefSNPreport_Submissions-Filter

History

History table is a listing of RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

RefSNPreport_History

History listing can be long, so use the "Filter" box to limit the display to only selected identifiers based on Associated ID or History Date, or Build number.

Publications

PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

RefSNPreport_Publications

Publications Filter

Publication list can be long, so use the "Filter" box to limit the display to selected citations based on PMID, Title, Author, Year or Journal.

RefSNPreport_Publications-Filter

Genomic regions, transcripts, and products

The "Genomic regions, transcripts, and products" section is the NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Visit the Sequence Viewer page for help with navigating inside the display and modifying the selection of displayed data tracks.
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.

RefSNPreport_GenomicView


Comparisons between new and old designs

To help users who are used to the classic RefSNP web page to make better use of the new design, comparisons between the new and old pages are summarized in a table below. In the table, screenshots of the above introduced sections are provided for both designs, and users can click on the thumbnails to see larger images. Note that there is no 'History' section on the classic page, and for several other sections (clinical significance, aliases, and publication) in the new design, their counterparts are combined and included in the 'summary' section in the old design.


Tag

Description

Organism Human, Homo sapiens
Position Variant map position on the latest assembly, i.e. GRCh38.p7. The assembly version will also include the GRC patch version 'p7'. The different patch versions, p6, p7, etc. does not disrupt the position on the primary assembly version GRCh38. See the online documentation () for further explanation of patches (https://www.ncbi.nlm.nih.gov/grc/help/patches/). Detailed list of all positions is available in the Variant Details and Aliases tabs.
NOTE: 
A dbSNP RefSNP is a cluster of variants that have the same position and type when mapped to the preferred top-level
sequence. The position is the deletion interval of the variant. It includes adjacent nucleotides in repeating regions
when the variant is shiftable, that is, it includes all nucleotides that could be affected by the variant. This is what
is displayed in the "Position" field in the 'Detail' section for a RefSNP. However, the web page displays alleles in
HGVS notation. HGVS right-shifts shiftable variants, so HGVS positions can differ from the displayed common "Position".
For example, consider inserting an A into a string of 5 A's that starts at position 11 in a sequence named SEQ1. The
canonical SPDI would be SEQ:11:AAAAA:AAAAAA (1-based for illustration). So the RefSNP position would be 11-15. The
corresponding HGVS expression using a right-shifted 1-based position of 15 would be SEQ1:g.15dup.
             
              
Alleles Reference and variant alleles for the rs. Detailed list of all alleles is available in the Variant Details and Aliases tabs.
Variation type One of the possible variation types: SNV : Single Nucleotide Variation; MNV : Multiple Nucleotide Variation; Insertion; Deletion; Indel : Insertion and Deletion; Identity; None.
Frequency Minor Allele Frequency (MAF) listed as a percentage representing a fraction, where the numerator is the number of samples observed and the denominator is the total number of samples, as reported in a given study.
Minor allele 'G' with a frequency of 0.0052 means that 'G' is observed 26 times among 5008 samples, as reported by the 1000 Genomes study. List of all reported frequencies for refrence and alternate alleles from various studies and populations is in the Frequency tab.
Clinical Significance Link to ClinVar, if any clinical significance data exist there, or an indication that there are no clinical significance data available in ClinVar for that rs.
If data are present in ClinVar, more links are available in the Clinical Significance tab.
Gene : Consequence Gene symbol (ie. LPL) and molecular consequence based on RefSeq mRNA or protein annotations.
Detailed list is available in the Variant Details tab.
Publications Number of citations where this rs was mentioned.
Detailed list is available in the Publications tab.
Genomic View Link to a graphical view of the RefSNP in the latest genomic context along with RefSeq mRNA and protein.
Use the zoom option within the Genomic View panel to inspect the nucleotides adjacent to the variant, and to see its neighbors.

Section

New Site

Classic Site

Summary RefSNPreport_Summary RefSNPreport_Summary
Variant Details RefSNPreport_VariantDetails RefSNPreport_VariantDetails
Clinical Significance RefSNPreport_ClinicalSignificance RefSNPreport_ClinicalSignificance
Frequency RefSNPreport_Frequency RefSNPreport_Frequency
Aliases RefSNPreport_Aliases RefSNPreport_Aliases
Submission RefSNPreport_Submissions RefSNPreport_Submissions
History RefSNPreport_History No History section
Publication RefSNPreport_Publications RefSNPreport_Publications


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Last updated: 2017-10-25T11:14:29-04:00