Name: rs12587588
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.

rs12587588

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr14:25748924 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.404809 (107149/264690, TOPMED)
C=0.402142 (55991/139232, GnomAD)
C=0.23144 (6540/28258, 14KJPN) (+ 14 more)
C=0.37035 (6996/18890, ALFA)
C=0.23305 (3906/16760, 8.3KJPN)
C=0.3837 (2457/6404, 1000G_30x)
C=0.3766 (1886/5008, 1000G)
C=0.3395 (1521/4480, Estonian)
C=0.2029 (594/2928, KOREAN)
C=0.1949 (357/1832, Korea1K)
C=0.382 (229/600, NorthernSweden)
C=0.222 (104/468, SGDP_PRJ)
C=0.464 (153/330, HapMap)
C=0.292 (63/216, Qatari)
C=0.165 (35/212, Vietnamese)
C=0.24 (12/50, Siberian)
C=0.35 (14/40, GENOME_DK)

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	18890	C=0.37035	T=0.62965
European	Sub	14286	C=0.31926	T=0.68074
African	Sub	2946	C=0.6375	T=0.3625
African Others	Sub	114	C=0.702	T=0.298
African American	Sub	2832	C=0.6349	T=0.3651
Asian	Sub	112	C=0.196	T=0.804
East Asian	Sub	86	C=0.17	T=0.83
Other Asian	Sub	26	C=0.27	T=0.73
Latin American 1	Sub	146	C=0.336	T=0.664
Latin American 2	Sub	610	C=0.269	T=0.731
South Asian	Sub	98	C=0.42	T=0.58
Other	Sub	692	C=0.406	T=0.594

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=0.404809	T=0.595191
gnomAD - Genomes	Global	Study-wide	139232	C=0.402142	T=0.597858
gnomAD - Genomes	European	Sub	75398	C=0.30596	T=0.69404
gnomAD - Genomes	African	Sub	41782	C=0.64274	T=0.35726
gnomAD - Genomes	American	Sub	13488	C=0.28292	T=0.71708
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	C=0.2354	T=0.7646
gnomAD - Genomes	East Asian	Sub	3110	C=0.2125	T=0.7875
gnomAD - Genomes	Other	Sub	2136	C=0.3787	T=0.6213
14KJPN	JAPANESE	Study-wide	28258	C=0.23144	T=0.76856
Allele Frequency Aggregator	Total	Global	18890	C=0.37035	T=0.62965
Allele Frequency Aggregator	European	Sub	14286	C=0.31926	T=0.68074
Allele Frequency Aggregator	African	Sub	2946	C=0.6375	T=0.3625
Allele Frequency Aggregator	Other	Sub	692	C=0.406	T=0.594
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.269	T=0.731
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.336	T=0.664
Allele Frequency Aggregator	Asian	Sub	112	C=0.196	T=0.804
Allele Frequency Aggregator	South Asian	Sub	98	C=0.42	T=0.58
8.3KJPN	JAPANESE	Study-wide	16760	C=0.23305	T=0.76695
1000Genomes_30x	Global	Study-wide	6404	C=0.3837	T=0.6163
1000Genomes_30x	African	Sub	1786	C=0.6646	T=0.3354
1000Genomes_30x	Europe	Sub	1266	C=0.2970	T=0.7030
1000Genomes_30x	South Asian	Sub	1202	C=0.3028	T=0.6972
1000Genomes_30x	East Asian	Sub	1170	C=0.2034	T=0.7966
1000Genomes_30x	American	Sub	980	C=0.298	T=0.702
1000Genomes	Global	Study-wide	5008	C=0.3766	T=0.6234
1000Genomes	African	Sub	1322	C=0.6679	T=0.3321
1000Genomes	East Asian	Sub	1008	C=0.2083	T=0.7917
1000Genomes	Europe	Sub	1006	C=0.2803	T=0.7197
1000Genomes	South Asian	Sub	978	C=0.312	T=0.688
1000Genomes	American	Sub	694	C=0.297	T=0.703
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.3395	T=0.6605
KOREAN population from KRGDB	KOREAN	Study-wide	2928	C=0.2029	A=0.0000, G=0.0000, T=0.7971
Korean Genome Project	KOREAN	Study-wide	1832	C=0.1949	T=0.8051
Northern Sweden	ACPOP	Study-wide	600	C=0.382	T=0.618
SGDP_PRJ	Global	Study-wide	468	C=0.222	T=0.778
HapMap	Global	Study-wide	330	C=0.464	T=0.536
HapMap	African	Sub	120	C=0.742	T=0.258
HapMap	American	Sub	120	C=0.358	T=0.642
HapMap	Asian	Sub	90	C=0.23	T=0.77
Qatari	Global	Study-wide	216	C=0.292	T=0.708
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.165	T=0.835
Siberian	Global	Study-wide	50	C=0.24	T=0.76
The Danish reference pan genome	Danish	Study-wide	40	C=0.35	T=0.65

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 14	NC_000014.9:g.25748924C>A
GRCh38.p14 chr 14	NC_000014.9:g.25748924C>G
GRCh38.p14 chr 14	NC_000014.9:g.25748924C>T
GRCh37.p13 chr 14	NC_000014.8:g.26218130C>A
GRCh37.p13 chr 14	NC_000014.8:g.26218130C>G
GRCh37.p13 chr 14	NC_000014.8:g.26218130C>T

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	G	T
GRCh38.p14 chr 14	NC_000014.9:g.25748924=	NC_000014.9:g.25748924C>A	NC_000014.9:g.25748924C>G	NC_000014.9:g.25748924C>T
GRCh37.p13 chr 14	NC_000014.8:g.26218130=	NC_000014.8:g.26218130C>A	NC_000014.8:g.26218130C>G	NC_000014.8:g.26218130C>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#.

66 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss19984308	Feb 28, 2004 (120)
2	SSAHASNP	ss21197118	Apr 05, 2004 (121)
3	ABI	ss40430011	Mar 14, 2006 (126)
4	BCMHGSC_JDW	ss89884402	Mar 24, 2008 (129)
5	HUMANGENOME_JCVI	ss96845720	Feb 06, 2009 (130)
6	BGI	ss106374482	Feb 06, 2009 (130)
7	1000GENOMES	ss108188394	Jan 23, 2009 (130)
8	1000GENOMES	ss115427501	Jan 25, 2009 (130)
9	ILLUMINA-UK	ss118385608	Feb 14, 2009 (130)
10	ENSEMBL	ss133880214	Dec 01, 2009 (131)
11	ENSEMBL	ss137086069	Dec 01, 2009 (131)
12	GMI	ss155547561	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss168969126	Jul 04, 2010 (132)
14	BCM-HGSC-SUB	ss206905884	Jul 04, 2010 (132)
15	1000GENOMES	ss226471127	Jul 14, 2010 (132)
16	1000GENOMES	ss236468984	Jul 15, 2010 (132)
17	1000GENOMES	ss242918657	Jul 15, 2010 (132)
18	GMI	ss281930187	May 04, 2012 (137)
19	GMI	ss286807648	Apr 25, 2013 (138)
20	PJP	ss291687580	May 09, 2011 (134)
21	SSMP	ss659642212	Apr 25, 2013 (138)
22	EVA-GONL	ss990946677	Aug 21, 2014 (142)
23	JMKIDD_LAB	ss1079504243	Aug 21, 2014 (142)
24	1000GENOMES	ss1350259776	Aug 21, 2014 (142)
25	DDI	ss1427363438	Apr 01, 2015 (144)
26	EVA_GENOME_DK	ss1577131552	Apr 01, 2015 (144)
27	EVA_DECODE	ss1694937720	Apr 01, 2015 (144)
28	HAMMER_LAB	ss1807839250	Sep 08, 2015 (146)
29	WEILL_CORNELL_DGM	ss1934322791	Feb 12, 2016 (147)
30	GENOMED	ss1967918740	Jul 19, 2016 (147)
31	JJLAB	ss2027936340	Sep 14, 2016 (149)
32	USC_VALOUEV	ss2156308369	Dec 20, 2016 (150)
33	HUMAN_LONGEVITY	ss2200442556	Dec 20, 2016 (150)
34	GRF	ss2700722917	Nov 08, 2017 (151)
35	GNOMAD	ss2925562966	Nov 08, 2017 (151)
36	SWEGEN	ss3011896926	Nov 08, 2017 (151)
37	BIOINF_KMB_FNS_UNIBA	ss3027791303	Nov 08, 2017 (151)
38	CSHL	ss3350718476	Nov 08, 2017 (151)
39	URBANLAB	ss3650164817	Oct 12, 2018 (152)
40	EGCUT_WGS	ss3679136537	Jul 13, 2019 (153)
41	EVA_DECODE	ss3696311383	Jul 13, 2019 (153)
42	ACPOP	ss3740216048	Jul 13, 2019 (153)
43	EVA	ss3752097906	Jul 13, 2019 (153)
44	PACBIO	ss3787614213	Jul 13, 2019 (153)
45	PACBIO	ss3792661005	Jul 13, 2019 (153)
46	PACBIO	ss3797545091	Jul 13, 2019 (153)
47	KHV_HUMAN_GENOMES	ss3817429369	Jul 13, 2019 (153)
48	EVA	ss3833821943	Apr 27, 2020 (154)
49	EVA	ss3840503010	Apr 27, 2020 (154)
50	EVA	ss3845990814	Apr 27, 2020 (154)
51	SGDP_PRJ	ss3881110196	Apr 27, 2020 (154)
52	KRGDB	ss3930083594	Apr 27, 2020 (154)
53	KOGIC	ss3974567723	Apr 27, 2020 (154)
54	TOPMED	ss4964146822	Apr 26, 2021 (155)
55	TOMMO_GENOMICS	ss5212390751	Apr 26, 2021 (155)
56	1000G_HIGH_COVERAGE	ss5295565037	Oct 16, 2022 (156)
57	HUGCELL_USP	ss5489687810	Oct 16, 2022 (156)
58	EVA	ss5511168808	Oct 16, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5595497307	Oct 16, 2022 (156)
60	SANFORD_IMAGENETICS	ss5655840372	Oct 16, 2022 (156)
61	TOMMO_GENOMICS	ss5764952009	Oct 16, 2022 (156)
62	YY_MCH	ss5814589322	Oct 16, 2022 (156)
63	EVA	ss5840847719	Oct 16, 2022 (156)
64	EVA	ss5850955572	Oct 16, 2022 (156)
65	EVA	ss5900596634	Oct 16, 2022 (156)
66	EVA	ss5947259755	Oct 16, 2022 (156)
67	1000Genomes	NC_000014.8 - 26218130	Oct 12, 2018 (152)
68	1000Genomes_30x	NC_000014.9 - 25748924	Oct 16, 2022 (156)
69	Genetic variation in the Estonian population	NC_000014.8 - 26218130	Oct 12, 2018 (152)
70	The Danish reference pan genome	NC_000014.8 - 26218130	Apr 27, 2020 (154)
71	gnomAD - Genomes	NC_000014.9 - 25748924	Apr 26, 2021 (155)
72	HapMap	NC_000014.9 - 25748924	Apr 27, 2020 (154)
73	KOREAN population from KRGDB	NC_000014.8 - 26218130	Apr 27, 2020 (154)
74	Korean Genome Project	NC_000014.9 - 25748924	Apr 27, 2020 (154)
75	Northern Sweden	NC_000014.8 - 26218130	Jul 13, 2019 (153)
76	Qatari	NC_000014.8 - 26218130	Apr 27, 2020 (154)
77	SGDP_PRJ	NC_000014.8 - 26218130	Apr 27, 2020 (154)
78	Siberian	NC_000014.8 - 26218130	Apr 27, 2020 (154)
79	8.3KJPN	NC_000014.8 - 26218130	Apr 26, 2021 (155)
80	14KJPN	NC_000014.9 - 25748924	Oct 16, 2022 (156)
81	TopMed	NC_000014.9 - 25748924	Apr 26, 2021 (155)
82	A Vietnamese Genetic Variation Database	NC_000014.8 - 26218130	Jul 13, 2019 (153)
83	ALFA	NC_000014.9 - 25748924	Apr 26, 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
37260988, ss3930083594	NC_000014.8:26218129:C:A	NC_000014.9:25748923:C:A	(self)
37260988, ss3930083594	NC_000014.8:26218129:C:G	NC_000014.9:25748923:C:G	(self)
ss89884402, ss108188394, ss115427501, ss118385608, ss168969126, ss206905884, ss281930187, ss286807648, ss291687580, ss1694937720	NC_000014.7:25287969:C:T	NC_000014.9:25748923:C:T	(self)
63210990, 24874785, 3524316, 37260988, 13500913, 16364721, 33127176, 8824723, 70360058, 7810454, ss226471127, ss236468984, ss242918657, ss659642212, ss990946677, ss1079504243, ss1350259776, ss1427363438, ss1577131552, ss1807839250, ss1934322791, ss1967918740, ss2027936340, ss2156308369, ss2700722917, ss2925562966, ss3011896926, ss3350718476, ss3679136537, ss3740216048, ss3752097906, ss3787614213, ss3792661005, ss3797545091, ss3833821943, ss3840503010, ss3881110196, ss3930083594, ss5212390751, ss5511168808, ss5655840372, ss5840847719, ss5947259755	NC_000014.8:26218129:C:T	NC_000014.9:25748923:C:T	(self)
83023242, 445733439, 1107889, 30945724, 98789113, 179692481, 4438613395, ss2200442556, ss3027791303, ss3650164817, ss3696311383, ss3817429369, ss3845990814, ss3974567723, ss4964146822, ss5295565037, ss5489687810, ss5595497307, ss5764952009, ss5814589322, ss5850955572, ss5900596634	NC_000014.9:25748923:C:T	NC_000014.9:25748923:C:T	(self)
ss19984308, ss21197118	NT_026437.10:6138257:C:T	NC_000014.9:25748923:C:T	(self)
ss40430011, ss96845720, ss106374482, ss133880214, ss137086069, ss155547561	NT_026437.12:7218129:C:T	NC_000014.9:25748923:C: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 rs12587588

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

rs12587588