Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs116395890

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:65225018 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.005319 (1408/264690, TOPMED)
T=0.001130 (280/247766, GnomAD_exome)
T=0.025902 (4824/186242, ALFA) (+ 8 more)
T=0.004743 (665/140218, GnomAD)
T=0.001475 (178/120658, ExAC)
T=0.00738 (581/78700, PAGE_STUDY)
T=0.00526 (66/12546, GO-ESP)
T=0.0056 (36/6404, 1000G_30x)
T=0.0054 (27/5008, 1000G)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
RGS9 : 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 202634 C=0.975794 T=0.024206
European Sub 165240 C=0.972597 T=0.027403
African Sub 11878 C=0.98577 T=0.01423
African Others Sub 436 C=0.986 T=0.014
African American Sub 11442 C=0.98575 T=0.01425
Asian Sub 6314 C=1.0000 T=0.0000
East Asian Sub 4468 C=1.0000 T=0.0000
Other Asian Sub 1846 C=1.0000 T=0.0000
Latin American 1 Sub 796 C=0.991 T=0.009
Latin American 2 Sub 984 C=0.999 T=0.001
South Asian Sub 270 C=1.000 T=0.000
Other Sub 17152 C=0.98834 T=0.01166


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 C=0.994681 T=0.005319
gnomAD - Exomes Global Study-wide 247766 C=0.998870 T=0.001130
gnomAD - Exomes European Sub 133058 C=0.999992 T=0.000008
gnomAD - Exomes Asian Sub 48580 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34522 C=0.99954 T=0.00046
gnomAD - Exomes African Sub 15488 C=0.98334 T=0.01666
gnomAD - Exomes Ashkenazi Jewish Sub 10064 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6054 C=0.9992 T=0.0008
Allele Frequency Aggregator Total Global 186242 C=0.974098 T=0.025902
Allele Frequency Aggregator European Sub 155118 C=0.970809 T=0.029191
Allele Frequency Aggregator Other Sub 15718 C=0.98753 T=0.01247
Allele Frequency Aggregator African Sub 7042 C=0.9869 T=0.0131
Allele Frequency Aggregator Asian Sub 6314 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 984 C=0.999 T=0.001
Allele Frequency Aggregator Latin American 1 Sub 796 C=0.991 T=0.009
Allele Frequency Aggregator South Asian Sub 270 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 140218 C=0.995257 T=0.004743
gnomAD - Genomes European Sub 75926 C=0.99995 T=0.00005
gnomAD - Genomes African Sub 42026 C=0.98491 T=0.01509
gnomAD - Genomes American Sub 13662 C=0.99876 T=0.00124
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2152 C=0.9954 T=0.0046
ExAC Global Study-wide 120658 C=0.998525 T=0.001475
ExAC Europe Sub 73292 C=0.99999 T=0.00001
ExAC Asian Sub 25110 C=1.00000 T=0.00000
ExAC American Sub 11574 C=0.99931 T=0.00069
ExAC African Sub 9782 C=0.9829 T=0.0171
ExAC Other Sub 900 C=0.998 T=0.002
The PAGE Study Global Study-wide 78700 C=0.99262 T=0.00738
The PAGE Study AfricanAmerican Sub 32514 C=0.98487 T=0.01513
The PAGE Study Mexican Sub 10810 C=0.99972 T=0.00028
The PAGE Study Asian Sub 8318 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 C=0.9958 T=0.0042
The PAGE Study NativeHawaiian Sub 4534 C=0.9996 T=0.0004
The PAGE Study Cuban Sub 4230 C=0.9981 T=0.0019
The PAGE Study Dominican Sub 3828 C=0.9914 T=0.0086
The PAGE Study CentralAmerican Sub 2450 C=0.9980 T=0.0020
The PAGE Study SouthAmerican Sub 1982 C=0.9975 T=0.0025
The PAGE Study NativeAmerican Sub 1260 C=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 12546 C=0.99474 T=0.00526
GO Exome Sequencing Project European American Sub 8416 C=1.0000 T=0.0000
GO Exome Sequencing Project African American Sub 4130 C=0.9840 T=0.0160
1000Genomes_30x Global Study-wide 6404 C=0.9944 T=0.0056
1000Genomes_30x African Sub 1786 C=0.9810 T=0.0190
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=0.998 T=0.002
1000Genomes Global Study-wide 5008 C=0.9946 T=0.0054
1000Genomes African Sub 1322 C=0.9803 T=0.0197
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=0.999 T=0.001
SGDP_PRJ Global Study-wide 2 C=0.5 T=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.65225018C>A
GRCh38.p14 chr 17 NC_000017.11:g.65225018C>T
GRCh37.p13 chr 17 NC_000017.10:g.63221136C>A
GRCh37.p13 chr 17 NC_000017.10:g.63221136C>T
RGS9 RefSeqGene NG_013021.2:g.92681C>A
RGS9 RefSeqGene NG_013021.2:g.92681C>T
Gene: RGS9, regulator of G protein signaling 9 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RGS9 transcript variant 3 NM_001165933.2:c. N/A Genic Downstream Transcript Variant
RGS9 transcript variant 1 NM_003835.4:c.1424C>A A [GCT] > D [GAT] Coding Sequence Variant
regulator of G-protein signaling 9 isoform 1 NP_003826.2:p.Ala475Asp A (Ala) > D (Asp) Missense Variant
RGS9 transcript variant 1 NM_003835.4:c.1424C>T A [GCT] > V [GTT] Coding Sequence Variant
regulator of G-protein signaling 9 isoform 1 NP_003826.2:p.Ala475Val A (Ala) > V (Val) Missense Variant
RGS9 transcript variant 2 NM_001081955.3:c.1415C>A A [GCT] > D [GAT] Coding Sequence Variant
regulator of G-protein signaling 9 isoform 2 NP_001075424.1:p.Ala472Asp A (Ala) > D (Asp) Missense Variant
RGS9 transcript variant 2 NM_001081955.3:c.1415C>T A [GCT] > V [GTT] Coding Sequence Variant
regulator of G-protein signaling 9 isoform 2 NP_001075424.1:p.Ala472Val A (Ala) > V (Val) 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: T (allele ID: 704303 )
ClinVar Accession Disease Names Clinical Significance
RCV000959451.6 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 C= A T
GRCh38.p14 chr 17 NC_000017.11:g.65225018= NC_000017.11:g.65225018C>A NC_000017.11:g.65225018C>T
GRCh37.p13 chr 17 NC_000017.10:g.63221136= NC_000017.10:g.63221136C>A NC_000017.10:g.63221136C>T
RGS9 RefSeqGene NG_013021.2:g.92681= NG_013021.2:g.92681C>A NG_013021.2:g.92681C>T
RGS9 transcript variant 1 NM_003835.4:c.1424= NM_003835.4:c.1424C>A NM_003835.4:c.1424C>T
RGS9 transcript variant 1 NM_003835.3:c.1424= NM_003835.3:c.1424C>A NM_003835.3:c.1424C>T
RGS9 transcript variant 2 NM_001081955.3:c.1415= NM_001081955.3:c.1415C>A NM_001081955.3:c.1415C>T
RGS9 transcript variant 2 NM_001081955.2:c.1415= NM_001081955.2:c.1415C>A NM_001081955.2:c.1415C>T
regulator of G-protein signaling 9 isoform 1 NP_003826.2:p.Ala475= NP_003826.2:p.Ala475Asp NP_003826.2:p.Ala475Val
regulator of G-protein signaling 9 isoform 2 NP_001075424.1:p.Ala472= NP_001075424.1:p.Ala472Asp NP_001075424.1:p.Ala472Val
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#.

42 SubSNP, 10 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss227616925 Jul 14, 2010 (132)
2 ILLUMINA ss480456698 May 04, 2012 (137)
3 ILLUMINA ss483653988 May 04, 2012 (137)
4 1000GENOMES ss491129809 May 04, 2012 (137)
5 EXOME_CHIP ss491526463 May 04, 2012 (137)
6 TISHKOFF ss565359342 Apr 25, 2013 (138)
7 NHLBI-ESP ss713404887 Apr 25, 2013 (138)
8 ILLUMINA ss780731341 Sep 08, 2015 (146)
9 ILLUMINA ss781235922 Sep 08, 2015 (146)
10 ILLUMINA ss783407737 Sep 08, 2015 (146)
11 1000GENOMES ss1359251121 Aug 21, 2014 (142)
12 EVA_EXAC ss1692922028 Apr 01, 2015 (144)
13 ILLUMINA ss1752234906 Sep 08, 2015 (146)
14 ILLUMINA ss1917921534 Feb 12, 2016 (147)
15 ILLUMINA ss1959761636 Feb 12, 2016 (147)
16 HUMAN_LONGEVITY ss2218034564 Dec 20, 2016 (150)
17 GNOMAD ss2742941050 Nov 08, 2017 (151)
18 GNOMAD ss2749842029 Nov 08, 2017 (151)
19 GNOMAD ss2951642001 Nov 08, 2017 (151)
20 AFFY ss2985102340 Nov 08, 2017 (151)
21 AFFY ss2985737811 Nov 08, 2017 (151)
22 ILLUMINA ss3627703668 Oct 12, 2018 (152)
23 ILLUMINA ss3634683098 Oct 12, 2018 (152)
24 ILLUMINA ss3640390408 Oct 12, 2018 (152)
25 ILLUMINA ss3644693208 Oct 12, 2018 (152)
26 ILLUMINA ss3653874068 Oct 12, 2018 (152)
27 ILLUMINA ss3744447712 Jul 13, 2019 (153)
28 ILLUMINA ss3744983356 Jul 13, 2019 (153)
29 PAGE_CC ss3771939180 Jul 13, 2019 (153)
30 ILLUMINA ss3772481116 Jul 13, 2019 (153)
31 KHV_HUMAN_GENOMES ss3820107772 Jul 13, 2019 (153)
32 EVA ss3825142932 Apr 27, 2020 (154)
33 SGDP_PRJ ss3886060712 Apr 27, 2020 (154)
34 TOPMED ss5041356759 Apr 26, 2021 (155)
35 1000G_HIGH_COVERAGE ss5303672075 Oct 16, 2022 (156)
36 EVA ss5428556958 Oct 16, 2022 (156)
37 HUGCELL_USP ss5496659083 Oct 16, 2022 (156)
38 1000G_HIGH_COVERAGE ss5607655499 Oct 16, 2022 (156)
39 SANFORD_IMAGENETICS ss5660397229 Oct 16, 2022 (156)
40 EVA ss5847804111 Oct 16, 2022 (156)
41 EVA ss5914531545 Oct 16, 2022 (156)
42 EVA ss5951791531 Oct 16, 2022 (156)
43 1000Genomes NC_000017.10 - 63221136 Oct 12, 2018 (152)
44 1000Genomes_30x NC_000017.11 - 65225018 Oct 16, 2022 (156)
45 ExAC NC_000017.10 - 63221136 Oct 12, 2018 (152)
46 gnomAD - Genomes NC_000017.11 - 65225018 Apr 26, 2021 (155)
47 gnomAD - Exomes NC_000017.10 - 63221136 Jul 13, 2019 (153)
48 GO Exome Sequencing Project NC_000017.10 - 63221136 Oct 12, 2018 (152)
49 The PAGE Study NC_000017.11 - 65225018 Jul 13, 2019 (153)
50 SGDP_PRJ NC_000017.10 - 63221136 Apr 27, 2020 (154)
51 TopMed NC_000017.11 - 65225018 Apr 26, 2021 (155)
52 ALFA NC_000017.11 - 65225018 Apr 26, 2021 (155)
53 ClinVar RCV000959451.6 Oct 16, 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
ss2218034564 NC_000017.11:65225017:C:A NC_000017.11:65225017:C:A (self)
ss483653988 NC_000017.9:60651597:C:T NC_000017.11:65225017:C:T (self)
72515987, 3376247, 12247707, 1599993, 38077692, ss227616925, ss480456698, ss491129809, ss491526463, ss565359342, ss713404887, ss780731341, ss781235922, ss783407737, ss1359251121, ss1692922028, ss1752234906, ss1917921534, ss1959761636, ss2742941050, ss2749842029, ss2951642001, ss2985102340, ss2985737811, ss3627703668, ss3634683098, ss3640390408, ss3644693208, ss3653874068, ss3744447712, ss3744983356, ss3772481116, ss3825142932, ss3886060712, ss5428556958, ss5660397229, ss5847804111, ss5951791531 NC_000017.10:63221135:C:T NC_000017.11:65225017:C:T (self)
RCV000959451.6, 95181434, 511775679, 1160649, 256902421, 13086323555, ss2218034564, ss3771939180, ss3820107772, ss5041356759, ss5303672075, ss5496659083, ss5607655499, ss5914531545 NC_000017.11:65225017:C:T NC_000017.11:65225017:C:T (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 rs116395890

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