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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs5975187

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:130384522 (GRCh38.p14) 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=0.008822 (2335/264690, TOPMED)
A=0.002118 (388/183163, GnomAD_exome)
A=0.001146 (188/164002, ALFA) (+ 8 more)
A=0.008068 (842/104368, GnomAD)
A=0.00257 (225/87615, ExAC)
A=0.00824 (87/10563, GO-ESP)
A=0.0040 (19/4805, 1000G_30x)
A=0.0045 (17/3775, 1000G)
A=0.002 (1/428, HapMap)
G=0.5 (1/2, SGDP_PRJ)
A=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
GPR119 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 164002 G=0.998854 A=0.001146
European Sub 138126 G=0.999978 A=0.000022
African Sub 6038 G=0.9707 A=0.0293
African Others Sub 206 G=0.966 A=0.034
African American Sub 5832 G=0.9709 A=0.0291
Asian Sub 6352 G=1.0000 A=0.0000
East Asian Sub 4502 G=1.0000 A=0.0000
Other Asian Sub 1850 G=1.0000 A=0.0000
Latin American 1 Sub 450 G=0.996 A=0.004
Latin American 2 Sub 956 G=1.000 A=0.000
South Asian Sub 280 G=1.000 A=0.000
Other Sub 11800 G=0.99949 A=0.00051


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=0.991178 A=0.008822
gnomAD - Exomes Global Study-wide 183163 G=0.997882 A=0.002118
gnomAD - Exomes European Sub 97656 G=0.99996 A=0.00004
gnomAD - Exomes Asian Sub 32939 G=0.99997 A=0.00003
gnomAD - Exomes American Sub 27422 G=0.99898 A=0.00102
gnomAD - Exomes African Sub 13158 G=0.97348 A=0.02652
gnomAD - Exomes Ashkenazi Jewish Sub 7467 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 4521 G=0.9987 A=0.0013
Allele Frequency Aggregator Total Global 164002 G=0.998854 A=0.001146
Allele Frequency Aggregator European Sub 138126 G=0.999978 A=0.000022
Allele Frequency Aggregator Other Sub 11800 G=0.99949 A=0.00051
Allele Frequency Aggregator Asian Sub 6352 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 6038 G=0.9707 A=0.0293
Allele Frequency Aggregator Latin American 2 Sub 956 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 450 G=0.996 A=0.004
Allele Frequency Aggregator South Asian Sub 280 G=1.000 A=0.000
gnomAD - Genomes Global Study-wide 104368 G=0.991932 A=0.008068
gnomAD - Genomes European Sub 57258 G=0.99997 A=0.00003
gnomAD - Genomes African Sub 31398 G=0.97404 A=0.02596
gnomAD - Genomes American Sub 9371 G=0.9982 A=0.0018
gnomAD - Genomes Ashkenazi Jewish Sub 2530 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 2250 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 1561 G=0.9949 A=0.0051
ExAC Global Study-wide 87615 G=0.99743 A=0.00257
ExAC Europe Sub 52472 G=0.99996 A=0.00004
ExAC Asian Sub 16686 G=1.00000 A=0.00000
ExAC American Sub 9318 G=0.9988 A=0.0012
ExAC African Sub 8508 G=0.9753 A=0.0247
ExAC Other Sub 631 G=0.997 A=0.003
GO Exome Sequencing Project Global Study-wide 10563 G=0.99176 A=0.00824
GO Exome Sequencing Project European American Sub 6728 G=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 3835 G=0.9773 A=0.0227
1000Genomes_30x Global Study-wide 4805 G=0.9960 A=0.0040
1000Genomes_30x African Sub 1328 G=0.9880 A=0.0120
1000Genomes_30x Europe Sub 961 G=1.000 A=0.000
1000Genomes_30x South Asian Sub 883 G=1.000 A=0.000
1000Genomes_30x East Asian Sub 878 G=1.000 A=0.000
1000Genomes_30x American Sub 755 G=0.996 A=0.004
1000Genomes Global Study-wide 3775 G=0.9955 A=0.0045
1000Genomes African Sub 1003 G=0.9860 A=0.0140
1000Genomes Europe Sub 766 G=1.000 A=0.000
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=0.994 A=0.006
HapMap Global Study-wide 428 G=0.998 A=0.002
HapMap African Sub 226 G=0.996 A=0.004
HapMap American Sub 116 G=1.000 A=0.000
HapMap Asian Sub 86 G=1.00 A=0.00
SGDP_PRJ Global Study-wide 2 G=0.5 A=0.5
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.p14 chr X NC_000023.11:g.130384522G>A
GRCh37.p13 chr X NC_000023.10:g.129518496G>A
GPR119 RefSeqGene NG_016404.1:g.6016C>T
Gene: GPR119, G protein-coupled receptor 119 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GPR119 transcript NM_178471.3:c.926C>T S [TCG] > L [TTG] Coding Sequence Variant
glucose-dependent insulinotropic receptor NP_848566.1:p.Ser309Leu S (Ser) > L (Leu) Missense 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.

Allele: A (allele ID: 717645 )
ClinVar Accession Disease Names Clinical Significance
RCV000961845.3 not provided Benign
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.p14 chr X NC_000023.11:g.130384522= NC_000023.11:g.130384522G>A
GRCh37.p13 chr X NC_000023.10:g.129518496= NC_000023.10:g.129518496G>A
GPR119 RefSeqGene NG_016404.1:g.6016= NG_016404.1:g.6016C>T
GPR119 transcript NM_178471.2:c.926= NM_178471.2:c.926C>T
GPR119 transcript NM_178471.3:c.926= NM_178471.3:c.926C>T
glucose-dependent insulinotropic receptor NP_848566.1:p.Ser309= NP_848566.1:p.Ser309Leu
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#.

50 SubSNP, 10 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8264751 Apr 21, 2003 (114)
2 ILLUMINA ss75014267 Dec 06, 2007 (129)
3 KRIBB_YJKIM ss119503129 Dec 01, 2009 (131)
4 ILLUMINA ss173953753 Jul 04, 2010 (132)
5 1000GENOMES ss341803602 May 09, 2011 (134)
6 NHLBI-ESP ss342559289 May 09, 2011 (134)
7 1000GENOMES ss491204308 May 04, 2012 (137)
8 GSK-GENETICS ss491283230 May 04, 2012 (137)
9 EXOME_CHIP ss491579462 May 04, 2012 (137)
10 ILLUMINA ss537326200 Sep 08, 2015 (146)
11 ILLUMINA ss780768205 Sep 08, 2015 (146)
12 ILLUMINA ss783447647 Sep 08, 2015 (146)
13 1000GENOMES ss1556174677 Apr 01, 2015 (144)
14 EVA_EXAC ss1694615222 Apr 01, 2015 (144)
15 ILLUMINA ss1752796400 Sep 08, 2015 (146)
16 ILLUMINA ss1917719675 Feb 12, 2016 (147)
17 ILLUMINA ss1945978922 Feb 12, 2016 (147)
18 ILLUMINA ss1958218137 Feb 12, 2016 (147)
19 ILLUMINA ss1958218138 Feb 12, 2016 (147)
20 HUMAN_LONGEVITY ss2320379926 Dec 20, 2016 (150)
21 GNOMAD ss2745553517 Nov 08, 2017 (151)
22 GNOMAD ss2746145341 Nov 08, 2017 (151)
23 GNOMAD ss2983419448 Nov 08, 2017 (151)
24 AFFY ss2985490654 Nov 08, 2017 (151)
25 ILLUMINA ss3023035873 Nov 08, 2017 (151)
26 ILLUMINA ss3023035874 Nov 08, 2017 (151)
27 ILLUMINA ss3630484103 Oct 12, 2018 (152)
28 ILLUMINA ss3630484104 Oct 12, 2018 (152)
29 ILLUMINA ss3635258604 Oct 12, 2018 (152)
30 ILLUMINA ss3638877148 Oct 12, 2018 (152)
31 ILLUMINA ss3640966076 Oct 12, 2018 (152)
32 ILLUMINA ss3643800809 Oct 12, 2018 (152)
33 ILLUMINA ss3645017897 Oct 12, 2018 (152)
34 ILLUMINA ss3653594064 Oct 12, 2018 (152)
35 ILLUMINA ss3653594065 Oct 12, 2018 (152)
36 ILLUMINA ss3654258204 Oct 12, 2018 (152)
37 ILLUMINA ss3726701312 Jul 14, 2019 (153)
38 ILLUMINA ss3744601232 Jul 14, 2019 (153)
39 ILLUMINA ss3745559132 Jul 14, 2019 (153)
40 ILLUMINA ss3773050758 Jul 14, 2019 (153)
41 KHV_HUMAN_GENOMES ss3823399123 Jul 14, 2019 (153)
42 EVA ss3825505718 Apr 27, 2020 (154)
43 SGDP_PRJ ss3892268994 Apr 27, 2020 (154)
44 TOPMED ss5137450692 Apr 26, 2021 (155)
45 1000G_HIGH_COVERAGE ss5313941334 Oct 13, 2022 (156)
46 HUGCELL_USP ss5505347824 Oct 13, 2022 (156)
47 1000G_HIGH_COVERAGE ss5623037941 Oct 13, 2022 (156)
48 SANFORD_IMAGENETICS ss5665892656 Oct 13, 2022 (156)
49 EVA ss5848238634 Oct 13, 2022 (156)
50 EVA ss5979011213 Oct 13, 2022 (156)
51 1000Genomes NC_000023.10 - 129518496 Oct 12, 2018 (152)
52 1000Genomes_30x NC_000023.11 - 130384522 Oct 13, 2022 (156)
53 ExAC NC_000023.10 - 129518496 Oct 12, 2018 (152)
54 gnomAD - Genomes NC_000023.11 - 130384522 Apr 26, 2021 (155)
55 gnomAD - Exomes NC_000023.10 - 129518496 Jul 14, 2019 (153)
56 GO Exome Sequencing Project NC_000023.10 - 129518496 Oct 12, 2018 (152)
57 HapMap NC_000023.11 - 130384522 Apr 27, 2020 (154)
58 SGDP_PRJ NC_000023.10 - 129518496 Apr 27, 2020 (154)
59 TopMed NC_000023.11 - 130384522 Apr 26, 2021 (155)
60 ALFA NC_000023.11 - 130384522 Apr 26, 2021 (155)
61 ClinVar RCV000961845.3 Oct 13, 2022 (156)
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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss491283230, ss3643800809 NC_000023.9:129346176:G:A NC_000023.11:130384521:G:A (self)
84133071, 10123923, 14883505, 1962472, 44285974, ss341803602, ss342559289, ss491204308, ss491579462, ss537326200, ss780768205, ss783447647, ss1556174677, ss1694615222, ss1752796400, ss1917719675, ss1945978922, ss1958218137, ss1958218138, ss2745553517, ss2746145341, ss2983419448, ss2985490654, ss3023035873, ss3023035874, ss3630484103, ss3630484104, ss3635258604, ss3638877148, ss3640966076, ss3645017897, ss3653594064, ss3653594065, ss3654258204, ss3744601232, ss3745559132, ss3773050758, ss3825505718, ss3892268994, ss5665892656, ss5848238634, ss5979011213 NC_000023.10:129518495:G:A NC_000023.11:130384521:G:A (self)
RCV000961845.3, 110563876, 591441621, 4037314, 701057049, 13519053597, ss2320379926, ss3726701312, ss3823399123, ss5137450692, ss5313941334, ss5505347824, ss5623037941 NC_000023.11:130384521:G:A NC_000023.11:130384521:G:A (self)
ss8264751, ss75014267, ss119503129, ss173953753 NT_011786.16:13786205:G:A NC_000023.11:130384521: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 rs5975187

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.post774+babeb33