Name: rs12329066
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.

rs12329066

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:17822 (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=0.118943 (31483/264690, TOPMED)
A=0.115106 (16116/140010, GnomAD)
A=0.02817 (796/28258, 14KJPN) (+ 13 more)
A=0.07565 (1479/19550, ALFA)
A=0.02840 (476/16760, 8.3KJPN)
A=0.1394 (893/6404, 1000G_30x)
A=0.1346 (674/5008, 1000G)
A=0.0122 (47/3854, ALSPAC)
A=0.0113 (42/3708, TWINSUK)
A=0.0461 (135/2930, KOREAN)
A=0.0502 (92/1832, Korea1K)
A=0.016 (16/998, GoNL)
A=0.037 (22/600, NorthernSweden)
A=0.088 (19/216, Qatari)
A=0.075 (16/214, Vietnamese)
G=0.34 (31/92, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	19550	G=0.92435	A=0.07565
European	Sub	14364	G=0.97967	A=0.02033
African	Sub	3380	G=0.6817	A=0.3183
African Others	Sub	114	G=0.667	A=0.333
African American	Sub	3266	G=0.6822	A=0.3178
Asian	Sub	146	G=0.952	A=0.048
East Asian	Sub	120	G=0.958	A=0.042
Other Asian	Sub	26	G=0.92	A=0.08
Latin American 1	Sub	146	G=0.897	A=0.103
Latin American 2	Sub	610	G=0.980	A=0.020
South Asian	Sub	104	G=0.990	A=0.010
Other	Sub	800	G=0.905	A=0.095

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=0.881057	A=0.118943
gnomAD - Genomes	Global	Study-wide	140010	G=0.884894	A=0.115106
gnomAD - Genomes	European	Sub	75916	G=0.98198	A=0.01802
gnomAD - Genomes	African	Sub	41854	G=0.67575	A=0.32425
gnomAD - Genomes	American	Sub	13642	G=0.95558	A=0.04442
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.9504	A=0.0496
gnomAD - Genomes	East Asian	Sub	3122	G=0.9343	A=0.0657
gnomAD - Genomes	Other	Sub	2152	G=0.9066	A=0.0934
14KJPN	JAPANESE	Study-wide	28258	G=0.97183	A=0.02817
Allele Frequency Aggregator	Total	Global	19550	G=0.92435	A=0.07565
Allele Frequency Aggregator	European	Sub	14364	G=0.97967	A=0.02033
Allele Frequency Aggregator	African	Sub	3380	G=0.6817	A=0.3183
Allele Frequency Aggregator	Other	Sub	800	G=0.905	A=0.095
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.980	A=0.020
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.897	A=0.103
Allele Frequency Aggregator	Asian	Sub	146	G=0.952	A=0.048
Allele Frequency Aggregator	South Asian	Sub	104	G=0.990	A=0.010
8.3KJPN	JAPANESE	Study-wide	16760	G=0.97160	A=0.02840
1000Genomes_30x	Global	Study-wide	6404	G=0.8606	A=0.1394
1000Genomes_30x	African	Sub	1786	G=0.6030	A=0.3970
1000Genomes_30x	Europe	Sub	1266	G=0.9810	A=0.0190
1000Genomes_30x	South Asian	Sub	1202	G=0.9534	A=0.0466
1000Genomes_30x	East Asian	Sub	1170	G=0.9573	A=0.0427
1000Genomes_30x	American	Sub	980	G=0.945	A=0.055
1000Genomes	Global	Study-wide	5008	G=0.8654	A=0.1346
1000Genomes	African	Sub	1322	G=0.6014	A=0.3986
1000Genomes	East Asian	Sub	1008	G=0.9623	A=0.0377
1000Genomes	Europe	Sub	1006	G=0.9801	A=0.0199
1000Genomes	South Asian	Sub	978	G=0.951	A=0.049
1000Genomes	American	Sub	694	G=0.941	A=0.059
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9878	A=0.0122
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9887	A=0.0113
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.9539	A=0.0461
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9498	A=0.0502
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.984	A=0.016
Northern Sweden	ACPOP	Study-wide	600	G=0.963	A=0.037
Qatari	Global	Study-wide	216	G=0.912	A=0.088
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.925	A=0.075
SGDP_PRJ	Global	Study-wide	92	G=0.34	A=0.66

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 2	NC_000002.12:g.17822G>A
GRCh37.p13 chr 2	NC_000002.11:g.17822G>A

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=	A
GRCh38.p14 chr 2	NC_000002.12:g.17822=	NC_000002.12:g.17822G>A
GRCh37.p13 chr 2	NC_000002.11:g.17822=	NC_000002.11:g.17822G>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#.

50 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss18805594	Feb 28, 2004 (120)
2	ILLUMINA-UK	ss117555062	Feb 14, 2009 (130)
3	COMPLETE_GENOMICS	ss162981117	Jul 04, 2010 (132)
4	BUSHMAN	ss199922892	Jul 04, 2010 (132)
5	1000GENOMES	ss219013221	Jul 14, 2010 (132)
6	TISHKOFF	ss555295631	Apr 25, 2013 (138)
7	SSMP	ss648872594	Apr 25, 2013 (138)
8	EVA-GONL	ss976396805	Aug 21, 2014 (142)
9	JMKIDD_LAB	ss1068790750	Aug 21, 2014 (142)
10	1000GENOMES	ss1295574388	Aug 21, 2014 (142)
11	EVA_DECODE	ss1585798199	Apr 01, 2015 (144)
12	EVA_UK10K_ALSPAC	ss1602626767	Apr 01, 2015 (144)
13	EVA_UK10K_TWINSUK	ss1645620800	Apr 01, 2015 (144)
14	HAMMER_LAB	ss1796107780	Sep 08, 2015 (146)
15	WEILL_CORNELL_DGM	ss1919623813	Feb 12, 2016 (147)
16	ILLUMINA	ss1958380292	Feb 12, 2016 (147)
17	JJLAB	ss2020339313	Sep 14, 2016 (149)
18	GRF	ss2702930155	Nov 08, 2017 (151)
19	GNOMAD	ss2768814595	Nov 08, 2017 (151)
20	SWEGEN	ss2988841589	Nov 08, 2017 (151)
21	ILLUMINA	ss3021931432	Nov 08, 2017 (151)
22	ILLUMINA	ss3652359445	Oct 11, 2018 (152)
23	EVA_DECODE	ss3703083868	Jul 12, 2019 (153)
24	ILLUMINA	ss3725749236	Jul 12, 2019 (153)
25	ACPOP	ss3728076129	Jul 12, 2019 (153)
26	EVA	ss3756245579	Jul 12, 2019 (153)
27	KHV_HUMAN_GENOMES	ss3800634304	Jul 12, 2019 (153)
28	EVA	ss3826772218	Apr 25, 2020 (154)
29	SGDP_PRJ	ss3851402785	Apr 25, 2020 (154)
30	KRGDB	ss3896770435	Apr 25, 2020 (154)
31	KOGIC	ss3946946605	Apr 25, 2020 (154)
32	TOPMED	ss4491455279	Apr 25, 2021 (155)
33	TOMMO_GENOMICS	ss5149496939	Apr 25, 2021 (155)
34	EVA	ss5237286422	Apr 25, 2021 (155)
35	1000G_HIGH_COVERAGE	ss5246618076	Oct 12, 2022 (156)
36	EVA	ss5326259077	Oct 12, 2022 (156)
37	HUGCELL_USP	ss5446965003	Oct 12, 2022 (156)
38	EVA	ss5506268403	Oct 12, 2022 (156)
39	1000G_HIGH_COVERAGE	ss5521110108	Oct 12, 2022 (156)
40	SANFORD_IMAGENETICS	ss5624433317	Oct 12, 2022 (156)
41	SANFORD_IMAGENETICS	ss5627923452	Oct 12, 2022 (156)
42	TOMMO_GENOMICS	ss5677567413	Oct 12, 2022 (156)
43	YY_MCH	ss5801853335	Oct 12, 2022 (156)
44	EVA	ss5819540846	Oct 12, 2022 (156)
45	EVA	ss5847179452	Oct 12, 2022 (156)
46	EVA	ss5847853374	Oct 12, 2022 (156)
47	EVA	ss5852352023	Oct 12, 2022 (156)
48	EVA	ss5928688349	Oct 12, 2022 (156)
49	EVA	ss5954107631	Oct 12, 2022 (156)
50	EVA	ss5979552924	Oct 12, 2022 (156)
51	1000Genomes	NC_000002.11 - 17822	Oct 11, 2018 (152)
52	1000Genomes_30x	NC_000002.12 - 17822	Oct 12, 2022 (156)
53	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 17822	Oct 11, 2018 (152)
54	gnomAD - Genomes	NC_000002.12 - 17822	Apr 25, 2021 (155)
55	Genome of the Netherlands Release 5	NC_000002.11 - 17822	Apr 25, 2020 (154)
56	KOREAN population from KRGDB	NC_000002.11 - 17822	Apr 25, 2020 (154)
57	Korean Genome Project	NC_000002.12 - 17822	Apr 25, 2020 (154)
58	Northern Sweden	NC_000002.11 - 17822	Jul 12, 2019 (153)
59	Qatari	NC_000002.11 - 17822	Apr 25, 2020 (154)
60	SGDP_PRJ	NC_000002.11 - 17822	Apr 25, 2020 (154)
61	8.3KJPN	NC_000002.11 - 17822	Apr 25, 2021 (155)
62	14KJPN	NC_000002.12 - 17822	Oct 12, 2022 (156)
63	TopMed	NC_000002.12 - 17822	Apr 25, 2021 (155)
64	UK 10K study - Twins	NC_000002.11 - 17822	Oct 11, 2018 (152)
65	A Vietnamese Genetic Variation Database	NC_000002.11 - 17822	Jul 12, 2019 (153)
66	ALFA	NC_000002.12 - 17822	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
ss117555062, ss162981117, ss199922892, ss1585798199	NC_000002.10:7821:G:A	NC_000002.12:17821:G:A	(self)
6464263, 3576849, 1572253, 3947829, 1360994, 1665743, 3419765, 7466246, 3576849, 780705, ss219013221, ss555295631, ss648872594, ss976396805, ss1068790750, ss1295574388, ss1602626767, ss1645620800, ss1796107780, ss1919623813, ss1958380292, ss2020339313, ss2702930155, ss2768814595, ss2988841589, ss3021931432, ss3652359445, ss3728076129, ss3756245579, ss3826772218, ss3851402785, ss3896770435, ss5149496939, ss5237286422, ss5326259077, ss5506268403, ss5624433317, ss5627923452, ss5819540846, ss5847179452, ss5847853374, ss5954107631, ss5979552924	NC_000002.11:17821:G:A	NC_000002.12:17821:G:A	(self)
8636043, 46149729, 3324606, 11404517, 295278158, 1804926755, ss3703083868, ss3725749236, ss3800634304, ss3946946605, ss4491455279, ss5246618076, ss5446965003, ss5521110108, ss5677567413, ss5801853335, ss5852352023, ss5928688349	NC_000002.12:17821:G:A	NC_000002.12:17821:G:A	(self)
ss18805594	NT_022327.13:7821:G:A	NC_000002.12:17821:G: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 rs12329066

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

rs12329066