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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.

rs201138699

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:65160511 (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=0.000642 (170/264690, TOPMED)
A=0.000589 (147/249556, GnomAD_exome)
A=0.000570 (80/140256, GnomAD) (+ 10 more)
A=0.000654 (79/120724, ExAC)
A=0.00122 (34/27878, ALFA)
A=0.00083 (10/12052, GO-ESP)
A=0.0003 (2/6404, 1000G_30x)
A=0.0004 (2/5008, 1000G)
A=0.0022 (10/4480, Estonian)
A=0.0003 (1/3854, ALSPAC)
A=0.0011 (4/3708, TWINSUK)
G=0.5 (1/2, SGDP_PRJ)
A=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RGS9 : Intron 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 27878 G=0.99878 A=0.00122
European Sub 20348 G=0.99857 A=0.00143
African Sub 3540 G=0.9994 A=0.0006
African Others Sub 122 G=1.000 A=0.000
African American Sub 3418 G=0.9994 A=0.0006
Asian Sub 168 G=1.000 A=0.000
East Asian Sub 112 G=1.000 A=0.000
Other Asian Sub 56 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 2968 G=0.9990 A=0.0010


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=0.999358 A=0.000642
gnomAD - Exomes Global Study-wide 249556 G=0.999411 A=0.000589
gnomAD - Exomes European Sub 134832 G=0.999199 A=0.000801
gnomAD - Exomes Asian Sub 48578 G=0.99959 A=0.00041
gnomAD - Exomes American Sub 34524 G=0.99965 A=0.00035
gnomAD - Exomes African Sub 15486 G=0.99961 A=0.00039
gnomAD - Exomes Ashkenazi Jewish Sub 10072 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6064 G=0.9998 A=0.0002
gnomAD - Genomes Global Study-wide 140256 G=0.999430 A=0.000570
gnomAD - Genomes European Sub 75958 G=0.99928 A=0.00072
gnomAD - Genomes African Sub 42036 G=0.99960 A=0.00040
gnomAD - Genomes American Sub 13654 G=0.99963 A=0.00037
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3130 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=0.9986 A=0.0014
ExAC Global Study-wide 120724 G=0.999346 A=0.000654
ExAC Europe Sub 73326 G=0.99917 A=0.00083
ExAC Asian Sub 25136 G=0.99952 A=0.00048
ExAC American Sub 11564 G=0.99974 A=0.00026
ExAC African Sub 9798 G=0.9997 A=0.0003
ExAC Other Sub 900 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 27878 G=0.99878 A=0.00122
Allele Frequency Aggregator European Sub 20348 G=0.99857 A=0.00143
Allele Frequency Aggregator African Sub 3540 G=0.9994 A=0.0006
Allele Frequency Aggregator Other Sub 2968 G=0.9990 A=0.0010
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 168 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
GO Exome Sequencing Project Global Study-wide 12052 G=0.99917 A=0.00083
GO Exome Sequencing Project European American Sub 8222 G=0.9989 A=0.0011
GO Exome Sequencing Project African American Sub 3830 G=0.9997 A=0.0003
1000Genomes_30x Global Study-wide 6404 G=0.9997 A=0.0003
1000Genomes_30x African Sub 1786 G=0.9994 A=0.0006
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=0.9992 A=0.0008
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9996 A=0.0004
1000Genomes African Sub 1322 G=0.9992 A=0.0008
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=0.999 A=0.001
1000Genomes American Sub 694 G=1.000 A=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9978 A=0.0022
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9997 A=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9989 A=0.0011
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 17 NC_000017.11:g.65160511G>A
GRCh37.p13 chr 17 NC_000017.10:g.63156629G>A
RGS9 RefSeqGene NG_013021.2:g.28174G>A
Gene: RGS9, regulator of G protein signaling 9 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RGS9 transcript variant 2 NM_001081955.3:c.313-25G>A N/A Intron Variant
RGS9 transcript variant 3 NM_001165933.2:c.313-25G>A N/A Intron Variant
RGS9 transcript variant 1 NM_003835.4:c.313-25G>A N/A Intron 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

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 17 NC_000017.11:g.65160511= NC_000017.11:g.65160511G>A
GRCh37.p13 chr 17 NC_000017.10:g.63156629= NC_000017.10:g.63156629G>A
RGS9 RefSeqGene NG_013021.2:g.28174= NG_013021.2:g.28174G>A
RGS9 transcript variant 2 NM_001081955.2:c.313-25= NM_001081955.2:c.313-25G>A
RGS9 transcript variant 2 NM_001081955.3:c.313-25= NM_001081955.3:c.313-25G>A
RGS9 transcript variant 3 NM_001165933.1:c.313-25= NM_001165933.1:c.313-25G>A
RGS9 transcript variant 3 NM_001165933.2:c.313-25= NM_001165933.2:c.313-25G>A
RGS9 transcript variant 1 NM_003835.3:c.313-25= NM_003835.3:c.313-25G>A
RGS9 transcript variant 1 NM_003835.4:c.313-25= NM_003835.4:c.313-25G>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#.

27 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss489121048 May 04, 2012 (137)
2 CLINSEQ_SNP ss491741707 May 04, 2012 (137)
3 NHLBI-ESP ss713404799 Apr 25, 2013 (138)
4 1000GENOMES ss1359248961 Aug 21, 2014 (142)
5 EVA_UK10K_ALSPAC ss1635950584 Apr 01, 2015 (144)
6 EVA_UK10K_TWINSUK ss1678944617 Apr 01, 2015 (144)
7 EVA_EXAC ss1692921594 Apr 01, 2015 (144)
8 EVA_DECODE ss1697304591 Apr 01, 2015 (144)
9 HUMAN_LONGEVITY ss2218030387 Dec 20, 2016 (150)
10 GNOMAD ss2742940423 Nov 08, 2017 (151)
11 GNOMAD ss2749841854 Nov 08, 2017 (151)
12 GNOMAD ss2951636718 Nov 08, 2017 (151)
13 EGCUT_WGS ss3682649369 Jul 13, 2019 (153)
14 EVA_DECODE ss3700764760 Jul 13, 2019 (153)
15 EVA ss3825142841 Apr 27, 2020 (154)
16 EVA ss3825904891 Apr 27, 2020 (154)
17 EVA ss3834939026 Apr 27, 2020 (154)
18 SGDP_PRJ ss3886059606 Apr 27, 2020 (154)
19 EVA ss3986737806 Apr 26, 2021 (155)
20 TOPMED ss5041340793 Apr 26, 2021 (155)
21 1000G_HIGH_COVERAGE ss5303670174 Oct 16, 2022 (156)
22 EVA ss5428553652 Oct 16, 2022 (156)
23 HUGCELL_USP ss5496657322 Oct 16, 2022 (156)
24 1000G_HIGH_COVERAGE ss5607652887 Oct 16, 2022 (156)
25 EVA ss5834184670 Oct 16, 2022 (156)
26 EVA ss5914529307 Oct 16, 2022 (156)
27 EVA ss5951790385 Oct 16, 2022 (156)
28 1000Genomes NC_000017.10 - 63156629 Oct 12, 2018 (152)
29 1000Genomes_30x NC_000017.11 - 65160511 Oct 16, 2022 (156)
30 The Avon Longitudinal Study of Parents and Children NC_000017.10 - 63156629 Oct 12, 2018 (152)
31 Genetic variation in the Estonian population NC_000017.10 - 63156629 Oct 12, 2018 (152)
32 ExAC NC_000017.10 - 63156629 Oct 12, 2018 (152)
33 gnomAD - Genomes NC_000017.11 - 65160511 Apr 26, 2021 (155)
34 gnomAD - Exomes NC_000017.10 - 63156629 Jul 13, 2019 (153)
35 GO Exome Sequencing Project NC_000017.10 - 63156629 Oct 12, 2018 (152)
36 SGDP_PRJ NC_000017.10 - 63156629 Apr 27, 2020 (154)
37 TopMed NC_000017.11 - 65160511 Apr 26, 2021 (155)
38 UK 10K study - Twins NC_000017.10 - 63156629 Oct 12, 2018 (152)
39 ALFA NC_000017.11 - 65160511 Apr 26, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss491741707, ss1697304591 NC_000017.9:60587090:G:A NC_000017.11:65160510:G:A (self)
72513736, 40179756, 28387617, 3375785, 12247047, 1599903, 38076586, 40179756, ss489121048, ss713404799, ss1359248961, ss1635950584, ss1678944617, ss1692921594, ss2742940423, ss2749841854, ss2951636718, ss3682649369, ss3825142841, ss3825904891, ss3834939026, ss3886059606, ss3986737806, ss5428553652, ss5834184670, ss5951790385 NC_000017.10:63156628:G:A NC_000017.11:65160510:G:A (self)
95178822, 511762262, 256886455, 11638098683, ss2218030387, ss3700764760, ss5041340793, ss5303670174, ss5496657322, ss5607652887, ss5914529307 NC_000017.11:65160510:G:A NC_000017.11:65160510: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 rs201138699

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.post761+d5e8e07