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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the Aliases tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs5588

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr20:49507620 (GRCh38.p12) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.0000 (1/78668, PAGE_STUDY)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PTGIS : 3 Prime UTR Variant
Publications
0 citations
Genomic View
See rs on genome
Help

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 nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p12 chr 20 NC_000020.11:g.49507620A>G
GRCh37.p13 chr 20 NC_000020.10:g.48124157A>G
PTGIS RefSeqGene NG_007940.1:g.65551T>C
Gene: PTGIS, prostaglandin I2 synthase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PTGIS transcript NM_000961.4:c. N/A 3 Prime UTR Variant
Help

Clinical Significance tab 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. 12274) to access full ClinVar report.

Not Reported in ClinVar
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. 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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
The PAGE Study Global Study-wide 78668 A=1.0000 G=0.0000
The PAGE Study AfricanAmerican Sub 32506 A=1.0000 G=0.0000
The PAGE Study Mexican Sub 10800 A=1.0000 G=0.0000
The PAGE Study Asian Sub 8318 A=1.000 G=0.000
The PAGE Study PuertoRican Sub 7918 A=1.000 G=0.000
The PAGE Study NativeHawaiian Sub 4532 A=1.000 G=0.000
The PAGE Study Cuban Sub 4226 A=1.000 G=0.000
The PAGE Study Dominican Sub 3824 A=1.000 G=0.000
The PAGE Study CentralAmerican Sub 2448 A=1.000 G=0.000
The PAGE Study SouthAmerican Sub 1982 A=1.000 G=0.000
The PAGE Study NativeAmerican Sub 1260 A=1.000 G=0.000
The PAGE Study SouthAsian Sub 854 A=1.00 G=0.00
Help

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".

Placement A= G Note
GRCh38.p12 chr 20 NC_000020.11:g.49507620= NC_000020.11:g.49507620A>G
GRCh37.p13 chr 20 NC_000020.10:g.48124157= NC_000020.10:g.48124157A>G
PTGIS RefSeqGene NG_007940.1:g.65551= NG_007940.1:g.65551T>C
PTGIS transcript NM_000961.4:c.*300= NM_000961.4:c.*300T>C
PTGIS transcript NM_000961.3:c.*300= NM_000961.3:c.*300T>C
Help

Submissions tab displays variations originally submitted to dbSNP, 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#.

37 SubSNP, 1 Frequency submissions
No Submitter Submission ID Date (Build)
1 ARAVINDA ss7054 Sep 19, 2000 (52)
2 ILLUMINA ss75256124 Dec 07, 2007 (129)
3 KRIBB_YJKIM ss119337635 Dec 01, 2009 (131)
4 ILLUMINA ss160743034 Dec 01, 2009 (131)
5 ILLUMINA ss173921659 Jul 04, 2010 (132)
6 ILLUMINA ss481148119 May 04, 2012 (137)
7 ILLUMINA ss481170386 May 04, 2012 (137)
8 ILLUMINA ss482159024 Sep 08, 2015 (146)
9 ILLUMINA ss485369220 May 04, 2012 (137)
10 ILLUMINA ss537311333 Sep 08, 2015 (146)
11 ILLUMINA ss778558066 Sep 08, 2015 (146)
12 ILLUMINA ss783130231 Sep 08, 2015 (146)
13 ILLUMINA ss784086751 Sep 08, 2015 (146)
14 ILLUMINA ss832389125 Sep 08, 2015 (146)
15 ILLUMINA ss834014896 Sep 08, 2015 (146)
16 ILLUMINA ss1752390443 Sep 08, 2015 (146)
17 ILLUMINA ss1946554349 Feb 12, 2016 (147)
18 ILLUMINA ss1959921857 Feb 12, 2016 (147)
19 ILLUMINA ss2633807212 Nov 08, 2017 (151)
20 ILLUMINA ss3022126371 Nov 08, 2017 (151)
21 ILLUMINA ss3625789230 Oct 12, 2018 (152)
22 ILLUMINA ss3628408455 Oct 12, 2018 (152)
23 ILLUMINA ss3631763175 Oct 12, 2018 (152)
24 ILLUMINA ss3633967808 Oct 12, 2018 (152)
25 ILLUMINA ss3634839588 Oct 12, 2018 (152)
26 ILLUMINA ss3635652836 Oct 12, 2018 (152)
27 ILLUMINA ss3636533468 Oct 12, 2018 (152)
28 ILLUMINA ss3637404935 Oct 12, 2018 (152)
29 ILLUMINA ss3638350268 Oct 12, 2018 (152)
30 ILLUMINA ss3640546886 Oct 12, 2018 (152)
31 ILLUMINA ss3643312678 Oct 12, 2018 (152)
32 ILLUMINA ss3644784750 Oct 12, 2018 (152)
33 ILLUMINA ss3652582984 Oct 12, 2018 (152)
34 ILLUMINA ss3725921803 Jul 13, 2019 (153)
35 ILLUMINA ss3745139480 Jul 13, 2019 (153)
36 PAGE_CC ss3772053098 Jul 13, 2019 (153)
37 ILLUMINA ss3772635639 Jul 13, 2019 (153)
38 The PAGE Study NC_000020.11 - 49507620 Jul 13, 2019 (153)
Help

History tab displays 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).

Associated ID History Updated (Build)
rs386599107 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss481148119, ss3643312678 NC_000020.9:47557563:A:G NC_000020.11:49507619:A:G (self)
ss481170386, ss482159024, ss485369220, ss537311333, ss778558066, ss783130231, ss784086751, ss832389125, ss834014896, ss1752390443, ss1946554349, ss1959921857, ss2633807212, ss3022126371, ss3625789230, ss3628408455, ss3631763175, ss3633967808, ss3634839588, ss3635652836, ss3636533468, ss3637404935, ss3638350268, ss3640546886, ss3644784750, ss3652582984, ss3745139480, ss3772635639 NC_000020.10:48124156:A:G NC_000020.11:49507619:A:G (self)
1274567, ss3725921803, ss3772053098 NC_000020.11:49507619:A:G NC_000020.11:49507619:A:G
ss7054, ss75256124, ss119337635, ss160743034, ss173921659 NT_011362.10:18320248:A:G NC_000020.11:49507619:A:G (self)
Help

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

No publications for rs5588

Genomic regions, transcripts, and products
Top Help

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

Software version is: 2.0.1.post308+0fe9b3b