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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 HGVS 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.

rs589

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrX:133184329 (GRCh38.p13) 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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.044297 (11725/264690, TOPMED)
A=0.039307 (4095/104180, GnomAD)
A=0.02208 (470/21290, ALFA) (+ 6 more)
A=0.0469 (177/3775, 1000G)
A=0.0003 (1/3708, TWINSUK)
A=0.0003 (1/2889, ALSPAC)
A=0.1181 (149/1262, HapMap)
A=0.028 (3/108, Qatari)
G=0.12 (2/16, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.p13 chr X NC_000023.11:g.133184329G>A
GRCh37.p13 chr X NC_000023.10:g.132318357G>A
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

ALFA Allele Frequency (New)
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 21290 G=0.97792 A=0.02208
European Sub 15536 G=0.99936 A=0.00064
African Sub 3576 G=0.8817 A=0.1183
African Others Sub 126 G=0.849 A=0.151
African American Sub 3450 G=0.8829 A=0.1171
Asian Sub 160 G=1.000 A=0.000
East Asian Sub 102 G=1.000 A=0.000
Other Asian Sub 58 G=1.00 A=0.00
Latin American 1 Sub 212 G=0.943 A=0.057
Latin American 2 Sub 754 G=0.989 A=0.011
South Asian Sub 110 G=1.000 A=0.000
Other Sub 942 G=0.982 A=0.018


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
TopMed Global Study-wide 264690 G=0.955703 A=0.044297
gnomAD - Genomes Global Study-wide 104180 G=0.960693 A=0.039307
gnomAD - Genomes European Sub 57253 G=0.99942 A=0.00058
gnomAD - Genomes African Sub 31229 G=0.87896 A=0.12104
gnomAD - Genomes American Sub 9357 G=0.9775 A=0.0225
gnomAD - Genomes Ashkenazi Jewish Sub 2522 G=0.9996 A=0.0004
gnomAD - Genomes East Asian Sub 2247 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 1572 G=0.9555 A=0.0445
1000Genomes Global Study-wide 3775 G=0.9531 A=0.0469
1000Genomes African Sub 1003 G=0.8345 A=0.1655
1000Genomes Europe Sub 766 G=0.997 A=0.003
1000Genomes East Asian Sub 764 G=1.000 A=0.000
1000Genomes South Asian Sub 718 G=1.000 A=0.000
1000Genomes American Sub 524 G=0.983 A=0.017
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9997 A=0.0003
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 2889 G=0.9997 A=0.0003
HapMap Global Study-wide 1262 G=0.8819 A=0.1181
HapMap African Sub 684 G=0.798 A=0.202
HapMap American Sub 318 G=0.972 A=0.028
HapMap Europe Sub 172 G=0.988 A=0.012
HapMap Asian Sub 88 G=1.00 A=0.00
Qatari Global Study-wide 108 G=0.972 A=0.028
SGDP_PRJ Global Study-wide 16 G=0.12 A=0.88
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 G= A
GRCh38.p13 chr X NC_000023.11:g.133184329= NC_000023.11:g.133184329G>A
GRCh37.p13 chr X NC_000023.10:g.132318357= NC_000023.10:g.132318357G>A
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#.

22 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss594 Sep 19, 2000 (36)
2 KWOK ss311689 Jul 12, 2000 (85)
3 SC_JCM ss570823 Jul 16, 2000 (80)
4 KWOK ss1255621 Oct 04, 2000 (86)
5 WI_SSAHASNP ss12039141 Jul 11, 2003 (116)
6 PERLEGEN ss23826129 Sep 20, 2004 (123)
7 ABI ss43563733 Mar 15, 2006 (126)
8 AFFY ss76829286 Dec 05, 2007 (129)
9 KRIBB_YJKIM ss104807683 Feb 05, 2009 (130)
10 1000GENOMES ss341813558 May 09, 2011 (134)
11 TISHKOFF ss567050932 Apr 25, 2013 (138)
12 JMKIDD_LAB ss1083143322 Aug 21, 2014 (142)
13 1000GENOMES ss1556231074 Apr 01, 2015 (144)
14 EVA_UK10K_ALSPAC ss1641566825 Apr 01, 2015 (144)
15 EVA_UK10K_TWINSUK ss1684560858 Apr 01, 2015 (144)
16 WEILL_CORNELL_DGM ss1939739910 Feb 12, 2016 (147)
17 HUMAN_LONGEVITY ss2320486856 Dec 20, 2016 (150)
18 GNOMAD ss2983569600 Nov 08, 2017 (151)
19 TOPMED ss3622446125 Nov 08, 2017 (151)
20 KHV_HUMAN_GENOMES ss3823410819 Jul 14, 2019 (153)
21 SGDP_PRJ ss3892294626 Apr 27, 2020 (154)
22 TOPMED ss5137937522 Apr 27, 2021 (155)
23 1000Genomes NC_000023.10 - 132318357 Oct 12, 2018 (152)
24 The Avon Longitudinal Study of Parents and Children NC_000023.10 - 132318357 Oct 12, 2018 (152)
25 gnomAD - Genomes NC_000023.11 - 133184329 Apr 27, 2021 (155)
26 HapMap NC_000023.11 - 133184329 Apr 27, 2020 (154)
27 Qatari NC_000023.10 - 132318357 Apr 27, 2020 (154)
28 SGDP_PRJ NC_000023.10 - 132318357 Apr 27, 2020 (154)
29 TopMed NC_000023.11 - 133184329 Apr 27, 2021 (155)
30 UK 10K study - Twins NC_000023.10 - 132318357 Oct 12, 2018 (152)
31 ALFA NC_000023.11 - 133184329 Apr 27, 2021 (155)
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)
rs242150 Sep 19, 2000 (85)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss76829286 NC_000023.9:132146022:G:A NC_000023.11:133184328:G:A (self)
84188974, 46372135, 21781832, 44311606, 46372135, ss341813558, ss567050932, ss1083143322, ss1556231074, ss1641566825, ss1684560858, ss1939739910, ss2983569600, ss3892294626 NC_000023.10:132318356:G:A NC_000023.11:133184328:G:A (self)
591795293, 4039219, 437643640, 701543879, 6903103674, ss2320486856, ss3622446125, ss3823410819, ss5137937522 NC_000023.11:133184328:G:A NC_000023.11:133184328:G:A (self)
ss12039141 NT_011786.13:7886835:G:A NC_000023.11:133184328:G:A (self)
ss594, ss311689, ss570823, ss1255621, ss23826129, ss43563733, ss104807683 NT_011786.16:16586066:G:A NC_000023.11:133184328:G:A (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 rs589

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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.post596+ae089ad