Name: rs12730335
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.

rs12730335

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:163237609 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.181688 (48091/264690, TOPMED)
A=0.197020 (27552/139844, GnomAD)
A=0.07673 (2168/28256, 14KJPN) (+ 15 more)
A=0.23923 (4519/18890, ALFA)
A=0.07482 (1254/16760, 8.3KJPN)
A=0.1427 (914/6404, 1000G_30x)
A=0.1448 (725/5008, 1000G)
A=0.3433 (1538/4480, Estonian)
A=0.2553 (984/3854, ALSPAC)
A=0.2330 (864/3708, TWINSUK)
A=0.0846 (248/2930, KOREAN)
A=0.235 (235/998, GoNL)
A=0.243 (146/600, NorthernSweden)
A=0.111 (24/216, Qatari)
C=0.487 (76/156, SGDP_PRJ)
A=0.33 (13/40, GENOME_DK)
C=0.50 (12/24, Siberian)
A=0.50 (12/24, 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	18890	C=0.76077	A=0.23923
European	Sub	14286	C=0.72407	A=0.27593
African	Sub	2946	C=0.9100	A=0.0900
African Others	Sub	114	C=0.912	A=0.088
African American	Sub	2832	C=0.9100	A=0.0900
Asian	Sub	112	C=0.929	A=0.071
East Asian	Sub	86	C=0.93	A=0.07
Other Asian	Sub	26	C=0.92	A=0.08
Latin American 1	Sub	146	C=0.788	A=0.212
Latin American 2	Sub	610	C=0.785	A=0.215
South Asian	Sub	98	C=0.83	A=0.17
Other	Sub	692	C=0.819	A=0.181

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	C=0.818312	A=0.181688
gnomAD - Genomes	Global	Study-wide	139844	C=0.802980	A=0.197020
gnomAD - Genomes	European	Sub	75712	C=0.74086	A=0.25914
gnomAD - Genomes	African	Sub	41902	C=0.90962	A=0.09038
gnomAD - Genomes	American	Sub	13632	C=0.80238	A=0.19762
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.7563	A=0.2437
gnomAD - Genomes	East Asian	Sub	3128	C=0.9233	A=0.0767
gnomAD - Genomes	Other	Sub	2150	C=0.8130	A=0.1870
14KJPN	JAPANESE	Study-wide	28256	C=0.92327	A=0.07673
Allele Frequency Aggregator	Total	Global	18890	C=0.76077	A=0.23923
Allele Frequency Aggregator	European	Sub	14286	C=0.72407	A=0.27593
Allele Frequency Aggregator	African	Sub	2946	C=0.9100	A=0.0900
Allele Frequency Aggregator	Other	Sub	692	C=0.819	A=0.181
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.785	A=0.215
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.788	A=0.212
Allele Frequency Aggregator	Asian	Sub	112	C=0.929	A=0.071
Allele Frequency Aggregator	South Asian	Sub	98	C=0.83	A=0.17
8.3KJPN	JAPANESE	Study-wide	16760	C=0.92518	A=0.07482
1000Genomes_30x	Global	Study-wide	6404	C=0.8573	A=0.1427
1000Genomes_30x	African	Sub	1786	C=0.9295	A=0.0705
1000Genomes_30x	Europe	Sub	1266	C=0.7638	A=0.2362
1000Genomes_30x	South Asian	Sub	1202	C=0.8286	A=0.1714
1000Genomes_30x	East Asian	Sub	1170	C=0.9171	A=0.0829
1000Genomes_30x	American	Sub	980	C=0.810	A=0.190
1000Genomes	Global	Study-wide	5008	C=0.8552	A=0.1448
1000Genomes	African	Sub	1322	C=0.9266	A=0.0734
1000Genomes	East Asian	Sub	1008	C=0.9137	A=0.0863
1000Genomes	Europe	Sub	1006	C=0.7594	A=0.2406
1000Genomes	South Asian	Sub	978	C=0.832	A=0.168
1000Genomes	American	Sub	694	C=0.805	A=0.195
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.6567	A=0.3433
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7447	A=0.2553
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7670	A=0.2330
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.9154	A=0.0846
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.765	A=0.235
Northern Sweden	ACPOP	Study-wide	600	C=0.757	A=0.243
Qatari	Global	Study-wide	216	C=0.889	A=0.111
SGDP_PRJ	Global	Study-wide	156	C=0.487	A=0.513
The Danish reference pan genome	Danish	Study-wide	40	C=0.68	A=0.33
Siberian	Global	Study-wide	24	C=0.50	A=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.163237609C>A
GRCh37.p13 chr 1	NC_000001.10:g.163207399C>A
RGS5 RefSeqGene	NG_027731.2:g.89183G>T
TRNT1P1 pseudogene	NG_006601.2:g.545C>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+686… NM_001254748.2:c.-281+68624G>T	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	C=	A
GRCh38.p14 chr 1	NC_000001.11:g.163237609=	NC_000001.11:g.163237609C>A
GRCh37.p13 chr 1	NC_000001.10:g.163207399=	NC_000001.10:g.163207399C>A
RGS5 RefSeqGene	NG_027731.2:g.89183=	NG_027731.2:g.89183G>T
TRNT1P1 pseudogene	NG_006601.2:g.545=	NG_006601.2:g.545C>A
RGS5 transcript variant 3	NM_001254748.1:c.-281+68624=	NM_001254748.1:c.-281+68624G>T
RGS5 transcript variant 3	NM_001254748.2:c.-281+68624=	NM_001254748.2:c.-281+68624G>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#.

54 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss20466833	Apr 05, 2004 (121)
2	ABI	ss41153806	Mar 14, 2006 (126)
3	HUMANGENOME_JCVI	ss97979491	Feb 04, 2009 (130)
4	ENSEMBL	ss139191426	Dec 01, 2009 (131)
5	COMPLETE_GENOMICS	ss164260066	Jul 04, 2010 (132)
6	COMPLETE_GENOMICS	ss167204920	Jul 04, 2010 (132)
7	BUSHMAN	ss199162441	Jul 04, 2010 (132)
8	GMI	ss276075616	May 04, 2012 (137)
9	1000GENOMES	ss328988686	May 09, 2011 (134)
10	SSMP	ss648455154	Apr 25, 2013 (138)
11	EVA-GONL	ss975746034	Aug 21, 2014 (142)
12	JMKIDD_LAB	ss1068314527	Aug 21, 2014 (142)
13	1000GENOMES	ss1293166917	Aug 21, 2014 (142)
14	DDI	ss1425997582	Apr 01, 2015 (144)
15	EVA_GENOME_DK	ss1574434019	Apr 01, 2015 (144)
16	EVA_DECODE	ss1585129393	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1601341349	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1644335382	Apr 01, 2015 (144)
19	WEILL_CORNELL_DGM	ss1918982380	Feb 12, 2016 (147)
20	JJLAB	ss2020005433	Sep 14, 2016 (149)
21	USC_VALOUEV	ss2148032217	Dec 20, 2016 (150)
22	HUMAN_LONGEVITY	ss2167019726	Dec 20, 2016 (150)
23	SYSTEMSBIOZJU	ss2624511830	Nov 08, 2017 (151)
24	GRF	ss2698008672	Nov 08, 2017 (151)
25	GNOMAD	ss2762006022	Nov 08, 2017 (151)
26	SWEGEN	ss2987852126	Nov 08, 2017 (151)
27	BIOINF_KMB_FNS_UNIBA	ss3023760010	Nov 08, 2017 (151)
28	CSHL	ss3343738648	Nov 08, 2017 (151)
29	URBANLAB	ss3646804679	Oct 11, 2018 (152)
30	EGCUT_WGS	ss3655791441	Jul 12, 2019 (153)
31	EVA_DECODE	ss3687901586	Jul 12, 2019 (153)
32	ACPOP	ss3727538131	Jul 12, 2019 (153)
33	EVA	ss3746881648	Jul 12, 2019 (153)
34	KHV_HUMAN_GENOMES	ss3799881940	Jul 12, 2019 (153)
35	EVA	ss3826455769	Apr 25, 2020 (154)
36	EVA	ss3836623012	Apr 25, 2020 (154)
37	EVA	ss3842032639	Apr 25, 2020 (154)
38	SGDP_PRJ	ss3850130797	Apr 25, 2020 (154)
39	KRGDB	ss3895358714	Apr 25, 2020 (154)
40	TOPMED	ss4470420950	Apr 25, 2021 (155)
41	TOMMO_GENOMICS	ss5146763228	Apr 25, 2021 (155)
42	1000G_HIGH_COVERAGE	ss5244502413	Oct 12, 2022 (156)
43	EVA	ss5322430484	Oct 12, 2022 (156)
44	HUGCELL_USP	ss5445066986	Oct 12, 2022 (156)
45	EVA	ss5506049257	Oct 12, 2022 (156)
46	1000G_HIGH_COVERAGE	ss5517934571	Oct 12, 2022 (156)
47	SANFORD_IMAGENETICS	ss5626710008	Oct 12, 2022 (156)
48	TOMMO_GENOMICS	ss5674043701	Oct 12, 2022 (156)
49	YY_MCH	ss5801313272	Oct 12, 2022 (156)
50	EVA	ss5832748636	Oct 12, 2022 (156)
51	EVA	ss5849133095	Oct 12, 2022 (156)
52	EVA	ss5910482621	Oct 12, 2022 (156)
53	EVA	ss5938507823	Oct 12, 2022 (156)
54	EVA	ss5979994459	Oct 12, 2022 (156)
55	1000Genomes	NC_000001.10 - 163207399	Oct 11, 2018 (152)
56	1000Genomes_30x	NC_000001.11 - 163237609	Oct 12, 2022 (156)
57	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 163207399	Oct 11, 2018 (152)
58	Genetic variation in the Estonian population	NC_000001.10 - 163207399	Oct 11, 2018 (152)
59	The Danish reference pan genome	NC_000001.10 - 163207399	Apr 25, 2020 (154)
60	gnomAD - Genomes	NC_000001.11 - 163237609	Apr 25, 2021 (155)
61	Genome of the Netherlands Release 5	NC_000001.10 - 163207399	Apr 25, 2020 (154)
62	KOREAN population from KRGDB	NC_000001.10 - 163207399	Apr 25, 2020 (154)
63	Northern Sweden	NC_000001.10 - 163207399	Jul 12, 2019 (153)
64	Qatari	NC_000001.10 - 163207399	Apr 25, 2020 (154)
65	SGDP_PRJ	NC_000001.10 - 163207399	Apr 25, 2020 (154)
66	Siberian	NC_000001.10 - 163207399	Apr 25, 2020 (154)
67	8.3KJPN	NC_000001.10 - 163207399	Apr 25, 2021 (155)
68	14KJPN	NC_000001.11 - 163237609	Oct 12, 2022 (156)
69	TopMed	NC_000001.11 - 163237609	Apr 25, 2021 (155)
70	UK 10K study - Twins	NC_000001.10 - 163207399	Oct 11, 2018 (152)
71	ALFA	NC_000001.11 - 163237609	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
ss164260066, ss167204920, ss199162441, ss276075616, ss1585129393	NC_000001.9:161474022:C:A	NC_000001.11:163237608:C:A	(self)
3966875, 2160799, 1529689, 1732919, 939324, 2536108, 822996, 1024310, 2147777, 548571, 4732535, 2160799, ss328988686, ss648455154, ss975746034, ss1068314527, ss1293166917, ss1425997582, ss1574434019, ss1601341349, ss1644335382, ss1918982380, ss2020005433, ss2148032217, ss2624511830, ss2698008672, ss2762006022, ss2987852126, ss3343738648, ss3655791441, ss3727538131, ss3746881648, ss3826455769, ss3836623012, ss3850130797, ss3895358714, ss5146763228, ss5322430484, ss5506049257, ss5626710008, ss5832748636, ss5938507823, ss5979994459	NC_000001.10:163207398:C:A	NC_000001.11:163237608:C:A	(self)
5460506, 28802326, 7880805, 34027285, 14822507832, ss2167019726, ss3023760010, ss3646804679, ss3687901586, ss3799881940, ss3842032639, ss4470420950, ss5244502413, ss5445066986, ss5517934571, ss5674043701, ss5801313272, ss5849133095, ss5910482621	NC_000001.11:163237608:C:A	NC_000001.11:163237608:C:A	(self)
ss41153806, ss97979491, ss139191426	NT_004487.19:14696040:C:A	NC_000001.11:163237608:C:A	(self)
ss20466833	NT_004668.16:1712870:C:A	NC_000001.11:163237608:C:A	(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 rs12730335

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

rs12730335