Name: rs12753561
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.

rs12753561

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:163071076 (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>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.241233 (63852/264690, TOPMED)
T=0.234562 (32834/139980, GnomAD)
T=0.21770 (6720/30868, ALFA) (+ 17 more)
T=0.45990 (12995/28256, 14KJPN)
T=0.46420 (7780/16760, 8.3KJPN)
T=0.3117 (1996/6404, 1000G_30x)
T=0.3171 (1588/5008, 1000G)
T=0.1980 (887/4480, Estonian)
T=0.2172 (837/3854, ALSPAC)
T=0.2201 (816/3708, TWINSUK)
T=0.4192 (1225/2922, KOREAN)
T=0.4110 (753/1832, Korea1K)
T=0.225 (225/998, GoNL)
T=0.248 (149/600, NorthernSweden)
G=0.405 (106/262, SGDP_PRJ)
T=0.250 (54/216, Qatari)
T=0.374 (80/214, Vietnamese)
G=0.48 (43/90, HapMap)
T=0.23 (9/40, GENOME_DK)
G=0.45 (10/22, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RGS4 : Intron Variant
Publications: 1 citation
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	30868	G=0.78230	T=0.21770
European	Sub	24738	G=0.78794	T=0.21206
African	Sub	3168	G=0.7380	T=0.2620
African Others	Sub	124	G=0.685	T=0.315
African American	Sub	3044	G=0.7401	T=0.2599
Asian	Sub	128	G=0.562	T=0.438
East Asian	Sub	100	G=0.53	T=0.47
Other Asian	Sub	28	G=0.68	T=0.32
Latin American 1	Sub	168	G=0.720	T=0.280
Latin American 2	Sub	700	G=0.824	T=0.176
South Asian	Sub	114	G=0.702	T=0.298
Other	Sub	1852	G=0.7927	T=0.2073

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.758767	T=0.241233
gnomAD - Genomes	Global	Study-wide	139980	G=0.765438	T=0.234562
gnomAD - Genomes	European	Sub	75842	G=0.78431	T=0.21569
gnomAD - Genomes	African	Sub	41952	G=0.73718	T=0.26282
gnomAD - Genomes	American	Sub	13620	G=0.77247	T=0.22753
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	G=0.8356	T=0.1644
gnomAD - Genomes	East Asian	Sub	3102	G=0.5819	T=0.4181
gnomAD - Genomes	Other	Sub	2148	G=0.7630	T=0.2370
Allele Frequency Aggregator	Total	Global	30868	G=0.78230	T=0.21770
Allele Frequency Aggregator	European	Sub	24738	G=0.78794	T=0.21206
Allele Frequency Aggregator	African	Sub	3168	G=0.7380	T=0.2620
Allele Frequency Aggregator	Other	Sub	1852	G=0.7927	T=0.2073
Allele Frequency Aggregator	Latin American 2	Sub	700	G=0.824	T=0.176
Allele Frequency Aggregator	Latin American 1	Sub	168	G=0.720	T=0.280
Allele Frequency Aggregator	Asian	Sub	128	G=0.562	T=0.438
Allele Frequency Aggregator	South Asian	Sub	114	G=0.702	T=0.298
14KJPN	JAPANESE	Study-wide	28256	G=0.54010	T=0.45990
8.3KJPN	JAPANESE	Study-wide	16760	G=0.53580	T=0.46420
1000Genomes_30x	Global	Study-wide	6404	G=0.6883	T=0.3117
1000Genomes_30x	African	Sub	1786	G=0.7111	T=0.2889
1000Genomes_30x	Europe	Sub	1266	G=0.7773	T=0.2227
1000Genomes_30x	South Asian	Sub	1202	G=0.5466	T=0.4534
1000Genomes_30x	East Asian	Sub	1170	G=0.6188	T=0.3812
1000Genomes_30x	American	Sub	980	G=0.789	T=0.211
1000Genomes	Global	Study-wide	5008	G=0.6829	T=0.3171
1000Genomes	African	Sub	1322	G=0.7057	T=0.2943
1000Genomes	East Asian	Sub	1008	G=0.6210	T=0.3790
1000Genomes	Europe	Sub	1006	G=0.7753	T=0.2247
1000Genomes	South Asian	Sub	978	G=0.549	T=0.451
1000Genomes	American	Sub	694	G=0.784	T=0.216
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.8020	T=0.1980
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.7828	T=0.2172
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7799	T=0.2201
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.5808	C=0.0000, T=0.4192
Korean Genome Project	KOREAN	Study-wide	1832	G=0.5890	T=0.4110
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.775	T=0.225
Northern Sweden	ACPOP	Study-wide	600	G=0.752	T=0.248
SGDP_PRJ	Global	Study-wide	262	G=0.405	T=0.595
Qatari	Global	Study-wide	216	G=0.750	T=0.250
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.626	T=0.374
HapMap	Global	Study-wide	90	G=0.48	T=0.52
HapMap	Asian	Sub	90	G=0.48	T=0.52
The Danish reference pan genome	Danish	Study-wide	40	G=0.78	T=0.23
Siberian	Global	Study-wide	22	G=0.45	T=0.55

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.163071076G>C
GRCh38.p14 chr 1	NC_000001.11:g.163071076G>T
GRCh37.p13 chr 1	NC_000001.10:g.163040866G>C
GRCh37.p13 chr 1	NC_000001.10:g.163040866G>T
RGS4 RefSeqGene	NG_023312.1:g.7471G>C
RGS4 RefSeqGene	NG_023312.1:g.7471G>T

Gene: RGS4, regulator of G protein signaling 4 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RGS4 transcript variant 1	NM_001102445.3:c.336-1319… NM_001102445.3:c.336-1319G>C	N/A	Intron Variant
RGS4 transcript variant 4	NM_001113381.1:c.45-1319G… NM_001113381.1:c.45-1319G>C	N/A	Intron Variant
RGS4 transcript variant 2	NM_005613.6:c.45-1319G>C	N/A	Intron Variant
RGS4 transcript variant 3	NM_001113380.1:c.	N/A	Genic Upstream 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	G=	C	T
GRCh38.p14 chr 1	NC_000001.11:g.163071076=	NC_000001.11:g.163071076G>C	NC_000001.11:g.163071076G>T
GRCh37.p13 chr 1	NC_000001.10:g.163040866=	NC_000001.10:g.163040866G>C	NC_000001.10:g.163040866G>T
RGS4 RefSeqGene	NG_023312.1:g.7471=	NG_023312.1:g.7471G>C	NG_023312.1:g.7471G>T
RGS4 transcript variant 1	NM_001102445.2:c.336-1319=	NM_001102445.2:c.336-1319G>C	NM_001102445.2:c.336-1319G>T
RGS4 transcript variant 1	NM_001102445.3:c.336-1319=	NM_001102445.3:c.336-1319G>C	NM_001102445.3:c.336-1319G>T
RGS4 transcript variant 4	NM_001113381.1:c.45-1319=	NM_001113381.1:c.45-1319G>C	NM_001113381.1:c.45-1319G>T
RGS4 transcript variant 2	NM_005613.5:c.45-1319=	NM_005613.5:c.45-1319G>C	NM_005613.5:c.45-1319G>T
RGS4 transcript variant 2	NM_005613.6:c.45-1319=	NM_005613.6:c.45-1319G>C	NM_005613.6:c.45-1319G>T

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#.

78 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss20577224	Apr 05, 2004 (121)
2	ABI	ss41118033	Mar 15, 2006 (126)
3	HGSV	ss78874492	Dec 07, 2007 (129)
4	HGSV	ss85218690	Dec 15, 2007 (130)
5	BCMHGSC_JDW	ss87845739	Mar 23, 2008 (129)
6	BGI	ss102791112	Dec 01, 2009 (131)
7	1000GENOMES	ss108645485	Jan 23, 2009 (130)
8	1000GENOMES	ss111245646	Jan 25, 2009 (130)
9	ILLUMINA-UK	ss119060093	Feb 15, 2009 (130)
10	ENSEMBL	ss138093053	Dec 01, 2009 (131)
11	ENSEMBL	ss139191724	Dec 01, 2009 (131)
12	GMI	ss155837442	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss164256487	Jul 04, 2010 (132)
14	BCM-HGSC-SUB	ss205062344	Jul 04, 2010 (132)
15	1000GENOMES	ss218681519	Jul 14, 2010 (132)
16	1000GENOMES	ss230754264	Jul 14, 2010 (132)
17	1000GENOMES	ss238397751	Jul 15, 2010 (132)
18	BL	ss253555931	May 09, 2011 (134)
19	GMI	ss276075069	May 04, 2012 (137)
20	PJP	ss290649399	May 09, 2011 (134)
21	ILLUMINA	ss482124222	May 04, 2012 (137)
22	ILLUMINA	ss482984311	May 04, 2012 (137)
23	ILLUMINA	ss534941796	Sep 08, 2015 (146)
24	TISHKOFF	ss554771731	Apr 25, 2013 (138)
25	SSMP	ss648454330	Apr 25, 2013 (138)
26	ILLUMINA	ss780113209	Sep 08, 2015 (146)
27	ILLUMINA	ss781942842	Sep 08, 2015 (146)
28	ILLUMINA	ss835596030	Sep 08, 2015 (146)
29	EVA-GONL	ss975744759	Aug 21, 2014 (142)
30	JMKIDD_LAB	ss1068313549	Aug 21, 2014 (142)
31	1000GENOMES	ss1293162272	Aug 21, 2014 (142)
32	DDI	ss1425997114	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1574433086	Apr 01, 2015 (144)
34	EVA_DECODE	ss1585128050	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1601338807	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1644332840	Apr 01, 2015 (144)
37	HAMMER_LAB	ss1795173033	Sep 08, 2015 (146)
38	WEILL_CORNELL_DGM	ss1918981238	Feb 12, 2016 (147)
39	GENOMED	ss1966881047	Jul 19, 2016 (147)
40	JJLAB	ss2020004732	Sep 14, 2016 (149)
41	USC_VALOUEV	ss2148031503	Dec 20, 2016 (150)
42	HUMAN_LONGEVITY	ss2167010127	Dec 20, 2016 (150)
43	SYSTEMSBIOZJU	ss2624511422	Nov 08, 2017 (151)
44	ILLUMINA	ss2632584198	Nov 08, 2017 (151)
45	GRF	ss2698007931	Nov 08, 2017 (151)
46	GNOMAD	ss2761993233	Nov 08, 2017 (151)
47	SWEGEN	ss2987850240	Nov 08, 2017 (151)
48	BIOINF_KMB_FNS_UNIBA	ss3023759580	Nov 08, 2017 (151)
49	CSHL	ss3343738048	Nov 08, 2017 (151)
50	ILLUMINA	ss3626224863	Oct 11, 2018 (152)
51	ILLUMINA	ss3630616550	Oct 11, 2018 (152)
52	ILLUMINA	ss3641619968	Oct 11, 2018 (152)
53	URBANLAB	ss3646804473	Oct 11, 2018 (152)
54	EGCUT_WGS	ss3655789404	Jul 12, 2019 (153)
55	EVA_DECODE	ss3687899426	Jul 12, 2019 (153)
56	ACPOP	ss3727537077	Jul 12, 2019 (153)
57	EVA	ss3746880197	Jul 12, 2019 (153)
58	KHV_HUMAN_GENOMES	ss3799880484	Jul 12, 2019 (153)
59	EVA	ss3826455117	Apr 25, 2020 (154)
60	EVA	ss3836622647	Apr 25, 2020 (154)
61	EVA	ss3842032277	Apr 25, 2020 (154)
62	SGDP_PRJ	ss3850128521	Apr 25, 2020 (154)
63	KRGDB	ss3895356120	Apr 25, 2020 (154)
64	KOGIC	ss3945775409	Apr 25, 2020 (154)
65	TOPMED	ss4470380212	Apr 25, 2021 (155)
66	TOMMO_GENOMICS	ss5146758229	Apr 25, 2021 (155)
67	1000G_HIGH_COVERAGE	ss5244498585	Oct 12, 2022 (156)
68	EVA	ss5314655795	Oct 12, 2022 (156)
69	EVA	ss5322423173	Oct 12, 2022 (156)
70	HUGCELL_USP	ss5445063482	Oct 12, 2022 (156)
71	1000G_HIGH_COVERAGE	ss5517928615	Oct 12, 2022 (156)
72	SANFORD_IMAGENETICS	ss5626707887	Oct 12, 2022 (156)
73	TOMMO_GENOMICS	ss5674037288	Oct 12, 2022 (156)
74	YY_MCH	ss5801312212	Oct 12, 2022 (156)
75	EVA	ss5832747027	Oct 12, 2022 (156)
76	EVA	ss5849132499	Oct 12, 2022 (156)
77	EVA	ss5910477942	Oct 12, 2022 (156)
78	EVA	ss5938505428	Oct 12, 2022 (156)
79	1000Genomes	NC_000001.10 - 163040866	Oct 11, 2018 (152)
80	1000Genomes_30x	NC_000001.11 - 163071076	Oct 12, 2022 (156)
81	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 163040866	Oct 11, 2018 (152)
82	Genetic variation in the Estonian population	NC_000001.10 - 163040866	Oct 11, 2018 (152)
83	The Danish reference pan genome	NC_000001.10 - 163040866	Apr 25, 2020 (154)
84	gnomAD - Genomes	NC_000001.11 - 163071076	Apr 25, 2021 (155)
85	Genome of the Netherlands Release 5	NC_000001.10 - 163040866	Apr 25, 2020 (154)
86	HapMap	NC_000001.11 - 163071076	Apr 25, 2020 (154)
87	KOREAN population from KRGDB	NC_000001.10 - 163040866	Apr 25, 2020 (154)
88	Korean Genome Project	NC_000001.11 - 163071076	Apr 25, 2020 (154)
89	Northern Sweden	NC_000001.10 - 163040866	Jul 12, 2019 (153)
90	Qatari	NC_000001.10 - 163040866	Apr 25, 2020 (154)
91	SGDP_PRJ	NC_000001.10 - 163040866	Apr 25, 2020 (154)
92	Siberian	NC_000001.10 - 163040866	Apr 25, 2020 (154)
93	8.3KJPN	NC_000001.10 - 163040866	Apr 25, 2021 (155)
94	14KJPN	NC_000001.11 - 163071076	Oct 12, 2022 (156)
95	TopMed	NC_000001.11 - 163071076	Apr 25, 2021 (155)
96	UK 10K study - Twins	NC_000001.10 - 163040866	Oct 11, 2018 (152)
97	A Vietnamese Genetic Variation Database	NC_000001.10 - 163040866	Jul 12, 2019 (153)
98	ALFA	NC_000001.11 - 163071076	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).

Associated ID	History Updated (Build)
rs60931229	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
2533514, ss3895356120	NC_000001.10:163040865:G:C	NC_000001.11:163071075:G:C	(self)
ss78874492, ss85218690	NC_000001.8:159772523:G:T	NC_000001.11:163071075:G:T	(self)
ss87845739, ss108645485, ss111245646, ss119060093, ss164256487, ss205062344, ss253555931, ss276075069, ss290649399, ss482124222, ss1585128050	NC_000001.9:161307489:G:T	NC_000001.11:163071075:G:T	(self)
3962063, 2158032, 1527652, 1732348, 938068, 2533514, 821942, 1023168, 2145501, 547857, 4727536, 2158032, 462680, ss218681519, ss230754264, ss238397751, ss482984311, ss534941796, ss554771731, ss648454330, ss780113209, ss781942842, ss835596030, ss975744759, ss1068313549, ss1293162272, ss1425997114, ss1574433086, ss1601338807, ss1644332840, ss1795173033, ss1918981238, ss1966881047, ss2020004732, ss2148031503, ss2624511422, ss2632584198, ss2698007931, ss2761993233, ss2987850240, ss3343738048, ss3626224863, ss3630616550, ss3641619968, ss3655789404, ss3727537077, ss3746880197, ss3826455117, ss3836622647, ss3850128521, ss3895356120, ss5146758229, ss5314655795, ss5322423173, ss5626707887, ss5832747027, ss5938505428	NC_000001.10:163040865:G:T	NC_000001.11:163071075:G:T	(self)
5454550, 28769901, 188932, 2153410, 7874392, 33986547, 1858550101, ss2167010127, ss3023759580, ss3646804473, ss3687899426, ss3799880484, ss3842032277, ss3945775409, ss4470380212, ss5244498585, ss5445063482, ss5517928615, ss5674037288, ss5801312212, ss5849132499, ss5910477942	NC_000001.11:163071075:G:T	NC_000001.11:163071075:G:T	(self)
ss41118033, ss102791112, ss138093053, ss139191724, ss155837442	NT_004487.19:14529507:G:T	NC_000001.11:163071075:G:T	(self)
ss20577224	NT_004668.16:1546337:G:T	NC_000001.11:163071075:G:T	(self)

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

1 citation for rs12753561

PMID	Title	Author	Year	Journal
25324626	Research in China on the molecular genetics of schizophrenia.	Cui D et al.	2012	Shanghai archives of psychiatry

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs12753561