Name: rs1553698
Published: September 21, 2022
License: Open Access

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.

rs1553698

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:163297560 (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: A>C / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.137198 (36315/264690, TOPMED)
T=0.149119 (20882/140036, GnomAD)
T=0.02806 (793/28256, 14KJPN) (+ 17 more)
T=0.17704 (3289/18578, ALFA)
T=0.02601 (436/16760, 8.3KJPN)
T=0.0898 (575/6404, 1000G_30x)
T=0.0899 (450/5008, 1000G)
T=0.2683 (1202/4480, Estonian)
T=0.1897 (731/3854, ALSPAC)
T=0.1772 (657/3708, TWINSUK)
T=0.0300 (88/2930, KOREAN)
T=0.175 (175/998, GoNL)
T=0.177 (106/600, NorthernSweden)
T=0.125 (41/328, HapMap)
T=0.046 (10/216, Qatari)
T=0.046 (10/216, Vietnamese)
A=0.483 (58/120, SGDP_PRJ)
T=0.20 (8/40, GENOME_DK)
A=0.50 (7/14, Siberian)
T=0.50 (7/14, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RGS5 : 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	18578	A=0.82296	C=0.00000, T=0.17704
European	Sub	14052	A=0.79462	C=0.00000, T=0.20538
African	Sub	2870	A=0.9390	C=0.0000, T=0.0610
African Others	Sub	112	A=0.911	C=0.000, T=0.089
African American	Sub	2758	A=0.9402	C=0.0000, T=0.0598
Asian	Sub	112	A=0.955	C=0.000, T=0.045
East Asian	Sub	86	A=0.95	C=0.00, T=0.05
Other Asian	Sub	26	A=0.96	C=0.00, T=0.04
Latin American 1	Sub	146	A=0.842	C=0.000, T=0.158
Latin American 2	Sub	610	A=0.834	C=0.000, T=0.166
South Asian	Sub	98	A=0.90	C=0.00, T=0.10
Other	Sub	690	A=0.871	C=0.000, T=0.129

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	A=0.862802	T=0.137198
gnomAD - Genomes	Global	Study-wide	140036	A=0.850881	T=0.149119
gnomAD - Genomes	European	Sub	75826	A=0.80538	T=0.19462
gnomAD - Genomes	African	Sub	41986	A=0.92771	T=0.07229
gnomAD - Genomes	American	Sub	13624	A=0.85070	T=0.14930
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.8029	T=0.1971
gnomAD - Genomes	East Asian	Sub	3128	A=0.9703	T=0.0297
gnomAD - Genomes	Other	Sub	2148	A=0.8566	T=0.1434
14KJPN	JAPANESE	Study-wide	28256	A=0.97194	T=0.02806
Allele Frequency Aggregator	Total	Global	18578	A=0.82296	C=0.00000, T=0.17704
Allele Frequency Aggregator	European	Sub	14052	A=0.79462	C=0.00000, T=0.20538
Allele Frequency Aggregator	African	Sub	2870	A=0.9390	C=0.0000, T=0.0610
Allele Frequency Aggregator	Other	Sub	690	A=0.871	C=0.000, T=0.129
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.834	C=0.000, T=0.166
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.842	C=0.000, T=0.158
Allele Frequency Aggregator	Asian	Sub	112	A=0.955	C=0.000, T=0.045
Allele Frequency Aggregator	South Asian	Sub	98	A=0.90	C=0.00, T=0.10
8.3KJPN	JAPANESE	Study-wide	16760	A=0.97399	T=0.02601
1000Genomes_30x	Global	Study-wide	6404	A=0.9102	T=0.0898
1000Genomes_30x	African	Sub	1786	A=0.9384	T=0.0616
1000Genomes_30x	Europe	Sub	1266	A=0.8246	T=0.1754
1000Genomes_30x	South Asian	Sub	1202	A=0.9443	T=0.0557
1000Genomes_30x	East Asian	Sub	1170	A=0.9786	T=0.0214
1000Genomes_30x	American	Sub	980	A=0.846	T=0.154
1000Genomes	Global	Study-wide	5008	A=0.9101	T=0.0899
1000Genomes	African	Sub	1322	A=0.9387	T=0.0613
1000Genomes	East Asian	Sub	1008	A=0.9772	T=0.0228
1000Genomes	Europe	Sub	1006	A=0.8181	T=0.1819
1000Genomes	South Asian	Sub	978	A=0.946	T=0.054
1000Genomes	American	Sub	694	A=0.841	T=0.159
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.7317	T=0.2683
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.8103	T=0.1897
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.8228	T=0.1772
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.9700	T=0.0300
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.825	T=0.175
Northern Sweden	ACPOP	Study-wide	600	A=0.823	T=0.177
HapMap	Global	Study-wide	328	A=0.875	T=0.125
HapMap	African	Sub	120	A=0.908	T=0.092
HapMap	American	Sub	120	A=0.800	T=0.200
HapMap	Asian	Sub	88	A=0.93	T=0.07
Qatari	Global	Study-wide	216	A=0.954	T=0.046
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.954	T=0.046
SGDP_PRJ	Global	Study-wide	120	A=0.483	T=0.517
The Danish reference pan genome	Danish	Study-wide	40	A=0.80	T=0.20
Siberian	Global	Study-wide	14	A=0.50	T=0.50

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 1	NC_000001.11:g.163297560A>C
GRCh38.p14 chr 1	NC_000001.11:g.163297560A>T
GRCh37.p13 chr 1	NC_000001.10:g.163267350A>C
GRCh37.p13 chr 1	NC_000001.10:g.163267350A>T
RGS5 RefSeqGene	NG_027731.2:g.29232T>G
RGS5 RefSeqGene	NG_027731.2:g.29232T>A

Gene: RGS5, regulator of G protein signaling 5 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RGS5 transcript variant 3	NM_001254748.2:c.-281+867… NM_001254748.2:c.-281+8673T>G	N/A	Intron Variant
RGS5 transcript variant 2	NM_001195303.3:c.	N/A	Genic Upstream Transcript Variant
RGS5 transcript variant 4	NM_001254749.2:c.	N/A	Genic Upstream Transcript Variant
RGS5 transcript variant 1	NM_003617.4:c.	N/A	Genic Upstream Transcript Variant
LOC127814295 transcript variant 23	NR_045630.2:n.	N/A	Genic Downstream Transcript Variant

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

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=	C	T
GRCh38.p14 chr 1	NC_000001.11:g.163297560=	NC_000001.11:g.163297560A>C	NC_000001.11:g.163297560A>T
GRCh37.p13 chr 1	NC_000001.10:g.163267350=	NC_000001.10:g.163267350A>C	NC_000001.10:g.163267350A>T
RGS5 RefSeqGene	NG_027731.2:g.29232=	NG_027731.2:g.29232T>G	NG_027731.2:g.29232T>A
RGS5 transcript variant 3	NM_001254748.1:c.-281+8673=	NM_001254748.1:c.-281+8673T>G	NM_001254748.1:c.-281+8673T>A
RGS5 transcript variant 3	NM_001254748.2:c.-281+8673=	NM_001254748.2:c.-281+8673T>G	NM_001254748.2:c.-281+8673T>A

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#.

53 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2396789	Oct 23, 2000 (88)
2	BCM_SSAHASNP	ss9825266	Jul 11, 2003 (116)
3	SSAHASNP	ss20560072	Apr 05, 2004 (121)
4	ABI	ss41219531	Mar 13, 2006 (126)
5	HUMANGENOME_JCVI	ss97979626	Feb 04, 2009 (130)
6	1000GENOMES	ss111248764	Jan 25, 2009 (130)
7	ILLUMINA-UK	ss119061004	Feb 15, 2009 (130)
8	ENSEMBL	ss139191066	Dec 01, 2009 (131)
9	COMPLETE_GENOMICS	ss164261895	Jul 04, 2010 (132)
10	BUSHMAN	ss199163130	Jul 04, 2010 (132)
11	1000GENOMES	ss218682396	Jul 14, 2010 (132)
12	1000GENOMES	ss230755066	Jul 14, 2010 (132)
13	1000GENOMES	ss238398367	Jul 15, 2010 (132)
14	GMI	ss276075875	May 04, 2012 (137)
15	PJP	ss290649774	May 09, 2011 (134)
16	SSMP	ss648455526	Apr 25, 2013 (138)
17	EVA-GONL	ss975746527	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1068314840	Aug 21, 2014 (142)
19	1000GENOMES	ss1293168512	Aug 21, 2014 (142)
20	EVA_GENOME_DK	ss1574434542	Apr 01, 2015 (144)
21	EVA_DECODE	ss1585129869	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1601342243	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1644336276	Apr 01, 2015 (144)
24	WEILL_CORNELL_DGM	ss1918982841	Feb 12, 2016 (147)
25	GENOMED	ss1966881552	Jul 19, 2016 (147)
26	JJLAB	ss2020005715	Sep 14, 2016 (149)
27	USC_VALOUEV	ss2148032512	Dec 20, 2016 (150)
28	HUMAN_LONGEVITY	ss2167022962	Dec 20, 2016 (150)
29	GNOMAD	ss2762010652	Nov 08, 2017 (151)
30	SWEGEN	ss2987852850	Nov 08, 2017 (151)
31	BIOINF_KMB_FNS_UNIBA	ss3023760198	Nov 08, 2017 (151)
32	CSHL	ss3343738930	Nov 08, 2017 (151)
33	URBANLAB	ss3646804848	Oct 11, 2018 (152)
34	EGCUT_WGS	ss3655792185	Jul 12, 2019 (153)
35	EVA_DECODE	ss3687902379	Jul 12, 2019 (153)
36	ACPOP	ss3727538592	Jul 12, 2019 (153)
37	EVA	ss3746882195	Jul 12, 2019 (153)
38	KHV_HUMAN_GENOMES	ss3799882524	Jul 12, 2019 (153)
39	SGDP_PRJ	ss3850131609	Apr 25, 2020 (154)
40	KRGDB	ss3895359665	Apr 25, 2020 (154)
41	TOPMED	ss4470435159	Apr 25, 2021 (155)
42	TOMMO_GENOMICS	ss5146764967	Apr 25, 2021 (155)
43	1000G_HIGH_COVERAGE	ss5244503894	Oct 12, 2022 (156)
44	EVA	ss5322432927	Oct 12, 2022 (156)
45	HUGCELL_USP	ss5445068242	Oct 12, 2022 (156)
46	EVA	ss5506049531	Oct 12, 2022 (156)
47	1000G_HIGH_COVERAGE	ss5517936758	Oct 12, 2022 (156)
48	SANFORD_IMAGENETICS	ss5626710853	Oct 12, 2022 (156)
49	TOMMO_GENOMICS	ss5674045892	Oct 12, 2022 (156)
50	YY_MCH	ss5801313719	Oct 12, 2022 (156)
51	EVA	ss5832749257	Oct 12, 2022 (156)
52	EVA	ss5910484241	Oct 12, 2022 (156)
53	EVA	ss5938508669	Oct 12, 2022 (156)
54	1000Genomes	NC_000001.10 - 163267350	Oct 11, 2018 (152)
55	1000Genomes_30x	NC_000001.11 - 163297560	Oct 12, 2022 (156)
56	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 163267350	Oct 11, 2018 (152)
57	Genetic variation in the Estonian population	NC_000001.10 - 163267350	Oct 11, 2018 (152)
58	The Danish reference pan genome	NC_000001.10 - 163267350	Apr 25, 2020 (154)
59	gnomAD - Genomes	NC_000001.11 - 163297560	Apr 25, 2021 (155)
60	Genome of the Netherlands Release 5	NC_000001.10 - 163267350	Apr 25, 2020 (154)
61	HapMap	NC_000001.11 - 163297560	Apr 25, 2020 (154)
62	KOREAN population from KRGDB	NC_000001.10 - 163267350	Apr 25, 2020 (154)
63	Northern Sweden	NC_000001.10 - 163267350	Jul 12, 2019 (153)
64	Qatari	NC_000001.10 - 163267350	Apr 25, 2020 (154)
65	SGDP_PRJ	NC_000001.10 - 163267350	Apr 25, 2020 (154)
66	Siberian	NC_000001.10 - 163267350	Apr 25, 2020 (154)
67	8.3KJPN	NC_000001.10 - 163267350	Apr 25, 2021 (155)
68	14KJPN	NC_000001.11 - 163297560	Oct 12, 2022 (156)
69	TopMed	NC_000001.11 - 163297560	Apr 25, 2021 (155)
70	UK 10K study - Twins	NC_000001.10 - 163267350	Oct 11, 2018 (152)
71	A Vietnamese Genetic Variation Database	NC_000001.10 - 163267350	Jul 12, 2019 (153)
72	ALFA	NC_000001.11 - 163297560	Apr 25, 2021 (155)

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
14203820991	NC_000001.11:163297559:A:C	NC_000001.11:163297559:A:C	(self)
ss111248764, ss119061004, ss164261895, ss199163130, ss276075875, ss290649774, ss1585129869	NC_000001.9:161533973:A:T	NC_000001.11:163297559:A:T	(self)
3968544, 2161801, 1530433, 1733170, 939800, 2537059, 823457, 1024771, 2148589, 548866, 4734274, 2161801, 463647, ss218682396, ss230755066, ss238398367, ss648455526, ss975746527, ss1068314840, ss1293168512, ss1574434542, ss1601342243, ss1644336276, ss1918982841, ss1966881552, ss2020005715, ss2148032512, ss2762010652, ss2987852850, ss3343738930, ss3655792185, ss3727538592, ss3746882195, ss3850131609, ss3895359665, ss5146764967, ss5322432927, ss5506049531, ss5626710853, ss5832749257, ss5938508669	NC_000001.10:163267349:A:T	NC_000001.11:163297559:A:T	(self)
5462693, 28813597, 189382, 7882996, 34041494, 14203820991, ss2167022962, ss3023760198, ss3646804848, ss3687902379, ss3799882524, ss4470435159, ss5244503894, ss5445068242, ss5517936758, ss5674045892, ss5801313719, ss5910484241	NC_000001.11:163297559:A:T	NC_000001.11:163297559:A:T	(self)
ss2396789, ss41219531, ss97979626, ss139191066	NT_004487.19:14755991:A:T	NC_000001.11:163297559:A:T	(self)
ss9825266	NT_004668.15:9637908:A:T	NC_000001.11:163297559:A:T	(self)
ss20560072	NT_004668.16:1772821:A:T	NC_000001.11:163297559:A:T	(self)

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

No publications for rs1553698

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1553698