Name: rs12079586
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.

rs12079586

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:189429508 (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: T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.062749 (16609/264690, TOPMED)
G=0.060380 (8464/140178, GnomAD)
G=0.03805 (2431/63888, ALFA) (+ 17 more)
G=0.00004 (1/28252, 14KJPN)
G=0.00006 (1/16758, 8.3KJPN)
G=0.0684 (438/6404, 1000G_30x)
G=0.0655 (328/5008, 1000G)
G=0.0172 (77/4480, Estonian)
G=0.0392 (151/3854, ALSPAC)
G=0.0361 (134/3708, TWINSUK)
G=0.0456 (95/2082, HGDP_Stanford)
G=0.0800 (124/1550, HapMap)
G=0.034 (34/998, GoNL)
G=0.055 (33/600, NorthernSweden)
G=0.032 (7/216, Qatari)
G=0.005 (1/214, Vietnamese)
T=0.48 (24/50, SGDP_PRJ)
G=0.00 (0/28, Ancient Sardinia)
T=0.5 (1/2, Siberian)
G=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105371657 : 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	63888	T=0.96195	G=0.03805
European	Sub	51616	T=0.97055	G=0.02945
African	Sub	4298	T=0.8637	G=0.1363
African Others	Sub	170	T=0.871	G=0.129
African American	Sub	4128	T=0.8634	G=0.1366
Asian	Sub	184	T=1.000	G=0.000
East Asian	Sub	142	T=1.000	G=0.000
Other Asian	Sub	42	T=1.00	G=0.00
Latin American 1	Sub	250	T=0.924	G=0.076
Latin American 2	Sub	1232	T=0.9683	G=0.0317
South Asian	Sub	4946	T=0.9588	G=0.0412
Other	Sub	1362	T=0.9537	G=0.0463

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	T=0.937251	G=0.062749
gnomAD - Genomes	Global	Study-wide	140178	T=0.939620	G=0.060380
gnomAD - Genomes	European	Sub	75944	T=0.97064	G=0.02936
gnomAD - Genomes	African	Sub	42002	T=0.86720	G=0.13280
gnomAD - Genomes	American	Sub	13642	T=0.96687	G=0.03313
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.9729	G=0.0271
gnomAD - Genomes	East Asian	Sub	3114	T=0.9997	G=0.0003
gnomAD - Genomes	Other	Sub	2152	T=0.9475	G=0.0525
Allele Frequency Aggregator	Total	Global	63888	T=0.96195	G=0.03805
Allele Frequency Aggregator	European	Sub	51616	T=0.97055	G=0.02945
Allele Frequency Aggregator	South Asian	Sub	4946	T=0.9588	G=0.0412
Allele Frequency Aggregator	African	Sub	4298	T=0.8637	G=0.1363
Allele Frequency Aggregator	Other	Sub	1362	T=0.9537	G=0.0463
Allele Frequency Aggregator	Latin American 2	Sub	1232	T=0.9683	G=0.0317
Allele Frequency Aggregator	Latin American 1	Sub	250	T=0.924	G=0.076
Allele Frequency Aggregator	Asian	Sub	184	T=1.000	G=0.000
14KJPN	JAPANESE	Study-wide	28252	T=0.99996	G=0.00004
8.3KJPN	JAPANESE	Study-wide	16758	T=0.99994	G=0.00006
1000Genomes_30x	Global	Study-wide	6404	T=0.9316	G=0.0684
1000Genomes_30x	African	Sub	1786	T=0.8326	G=0.1674
1000Genomes_30x	Europe	Sub	1266	T=0.9676	G=0.0324
1000Genomes_30x	South Asian	Sub	1202	T=0.9476	G=0.0524
1000Genomes_30x	East Asian	Sub	1170	T=0.9949	G=0.0051
1000Genomes_30x	American	Sub	980	T=0.970	G=0.030
1000Genomes	Global	Study-wide	5008	T=0.9345	G=0.0655
1000Genomes	African	Sub	1322	T=0.8374	G=0.1626
1000Genomes	East Asian	Sub	1008	T=0.9950	G=0.0050
1000Genomes	Europe	Sub	1006	T=0.9672	G=0.0328
1000Genomes	South Asian	Sub	978	T=0.948	G=0.052
1000Genomes	American	Sub	694	T=0.965	G=0.035
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9828	G=0.0172
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9608	G=0.0392
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9639	G=0.0361
HGDP-CEPH-db Supplement 1	Global	Study-wide	2082	T=0.9544	G=0.0456
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	468	T=1.000	G=0.000
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	T=0.952	G=0.048
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	T=0.954	G=0.046
HGDP-CEPH-db Supplement 1	Europe	Sub	320	T=0.969	G=0.031
HGDP-CEPH-db Supplement 1	Africa	Sub	242	T=0.864	G=0.136
HGDP-CEPH-db Supplement 1	America	Sub	216	T=1.000	G=0.000
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	T=0.78	G=0.22
HapMap	Global	Study-wide	1550	T=0.9200	G=0.0800
HapMap	African	Sub	686	T=0.870	G=0.130
HapMap	American	Sub	600	T=0.945	G=0.055
HapMap	Europe	Sub	176	T=0.989	G=0.011
HapMap	Asian	Sub	88	T=1.00	G=0.00
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.966	G=0.034
Northern Sweden	ACPOP	Study-wide	600	T=0.945	G=0.055
Qatari	Global	Study-wide	216	T=0.968	G=0.032
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.995	G=0.005
SGDP_PRJ	Global	Study-wide	50	T=0.48	G=0.52
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	28	T=1.00	G=0.00
Siberian	Global	Study-wide	2	T=0.5	G=0.5

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.189429508T>G
GRCh37.p13 chr 1	NC_000001.10:g.189398638T>G

Gene: LOC105371657, uncharacterized LOC105371657 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105371657 transcript variant X1	XR_002958413.2:n.	N/A	Intron Variant
LOC105371657 transcript variant X2	XR_001738343.2: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	T=	G
GRCh38.p14 chr 1	NC_000001.11:g.189429508=	NC_000001.11:g.189429508T>G
GRCh37.p13 chr 1	NC_000001.10:g.189398638=	NC_000001.10:g.189398638T>G

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#.

63 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss18178338	Feb 28, 2004 (120)
2	ILLUMINA	ss66734066	Dec 01, 2006 (127)
3	ILLUMINA	ss66980567	Dec 01, 2006 (127)
4	ILLUMINA	ss67153024	Dec 01, 2006 (127)
5	ILLUMINA	ss70404682	May 18, 2007 (127)
6	ILLUMINA	ss70554758	May 24, 2008 (130)
7	ILLUMINA	ss71091462	May 18, 2007 (127)
8	ILLUMINA	ss75690616	Dec 07, 2007 (129)
9	KRIBB_YJKIM	ss85180638	Dec 14, 2007 (130)
10	ILLUMINA	ss121534640	Dec 01, 2009 (131)
11	ILLUMINA	ss153127336	Dec 01, 2009 (131)
12	ILLUMINA	ss159202844	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss167380896	Jul 04, 2010 (132)
14	ILLUMINA	ss170039730	Jul 04, 2010 (132)
15	ILLUMINA	ss171840195	Jul 04, 2010 (132)
16	1000GENOMES	ss218782030	Jul 14, 2010 (132)
17	1000GENOMES	ss230827071	Jul 14, 2010 (132)
18	ILLUMINA	ss536752796	Sep 08, 2015 (146)
19	TISHKOFF	ss554970967	Apr 25, 2013 (138)
20	ILLUMINA	ss825373956	Jul 19, 2016 (147)
21	ILLUMINA	ss832715291	Jul 12, 2019 (153)
22	EVA-GONL	ss975937837	Aug 21, 2014 (142)
23	JMKIDD_LAB	ss1068455991	Aug 21, 2014 (142)
24	1000GENOMES	ss1293892356	Aug 21, 2014 (142)
25	EVA_DECODE	ss1585330934	Apr 01, 2015 (144)
26	EVA_UK10K_ALSPAC	ss1601730510	Apr 01, 2015 (144)
27	EVA_UK10K_TWINSUK	ss1644724543	Apr 01, 2015 (144)
28	EVA_SVP	ss1712390304	Apr 01, 2015 (144)
29	WEILL_CORNELL_DGM	ss1919172587	Feb 12, 2016 (147)
30	JJLAB	ss2020103287	Sep 14, 2016 (149)
31	ILLUMINA	ss2094988676	Dec 20, 2016 (150)
32	USC_VALOUEV	ss2148130733	Dec 20, 2016 (150)
33	HUMAN_LONGEVITY	ss2168524622	Dec 20, 2016 (150)
34	GNOMAD	ss2764053117	Nov 08, 2017 (151)
35	SWEGEN	ss2988140281	Nov 08, 2017 (151)
36	CSHL	ss3343823239	Nov 08, 2017 (151)
37	ILLUMINA	ss3626265967	Oct 11, 2018 (152)
38	ILLUMINA	ss3637802727	Oct 11, 2018 (152)
39	ILLUMINA	ss3638917145	Oct 11, 2018 (152)
40	ILLUMINA	ss3639457138	Oct 11, 2018 (152)
41	ILLUMINA	ss3642810417	Oct 11, 2018 (152)
42	ILLUMINA	ss3651501407	Oct 11, 2018 (152)
43	EGCUT_WGS	ss3656093724	Jul 12, 2019 (153)
44	EVA_DECODE	ss3688251575	Jul 12, 2019 (153)
45	ACPOP	ss3727694403	Jul 12, 2019 (153)
46	EVA	ss3747102727	Jul 12, 2019 (153)
47	KHV_HUMAN_GENOMES	ss3800106578	Jul 12, 2019 (153)
48	HGDP	ss3847357294	Apr 25, 2020 (154)
49	SGDP_PRJ	ss3850504717	Apr 25, 2020 (154)
50	EVA	ss3984840629	Apr 25, 2021 (155)
51	EVA	ss4016951848	Apr 25, 2021 (155)
52	TOPMED	ss4476830016	Apr 25, 2021 (155)
53	TOMMO_GENOMICS	ss5147567828	Apr 25, 2021 (155)
54	1000G_HIGH_COVERAGE	ss5245131843	Oct 12, 2022 (156)
55	EVA	ss5323581732	Oct 12, 2022 (156)
56	HUGCELL_USP	ss5445632747	Oct 12, 2022 (156)
57	EVA	ss5506119258	Oct 12, 2022 (156)
58	1000G_HIGH_COVERAGE	ss5518886885	Oct 12, 2022 (156)
59	SANFORD_IMAGENETICS	ss5627069988	Oct 12, 2022 (156)
60	TOMMO_GENOMICS	ss5675078579	Oct 12, 2022 (156)
61	EVA	ss5832996194	Oct 12, 2022 (156)
62	EVA	ss5911211711	Oct 12, 2022 (156)
63	EVA	ss5938889778	Oct 12, 2022 (156)
64	1000Genomes	NC_000001.10 - 189398638	Oct 11, 2018 (152)
65	1000Genomes_30x	NC_000001.11 - 189429508	Oct 12, 2022 (156)
66	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 189398638	Oct 11, 2018 (152)
67	Genetic variation in the Estonian population	NC_000001.10 - 189398638	Oct 11, 2018 (152)
68	gnomAD - Genomes	NC_000001.11 - 189429508	Apr 25, 2021 (155)
69	Genome of the Netherlands Release 5	NC_000001.10 - 189398638	Apr 25, 2020 (154)
70	HGDP-CEPH-db Supplement 1	NC_000001.9 - 187665261	Apr 25, 2020 (154)
71	HapMap	NC_000001.11 - 189429508	Apr 25, 2020 (154)
72	Northern Sweden	NC_000001.10 - 189398638	Jul 12, 2019 (153)
73	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000001.10 - 189398638	Apr 25, 2021 (155)
74	Qatari	NC_000001.10 - 189398638	Apr 25, 2020 (154)
75	SGDP_PRJ	NC_000001.10 - 189398638	Apr 25, 2020 (154)
76	Siberian	NC_000001.10 - 189398638	Apr 25, 2020 (154)
77	8.3KJPN	NC_000001.10 - 189398638	Apr 25, 2021 (155)
78	14KJPN	NC_000001.11 - 189429508	Oct 12, 2022 (156)
79	TopMed	NC_000001.11 - 189429508	Apr 25, 2021 (155)
80	UK 10K study - Twins	NC_000001.10 - 189398638	Oct 11, 2018 (152)
81	A Vietnamese Genetic Variation Database	NC_000001.10 - 189398638	Jul 12, 2019 (153)
82	ALFA	NC_000001.11 - 189429508	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)
rs57829314	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss3638917145, ss3639457138	NC_000001.8:186130294:T:G	NC_000001.11:189429507:T:G	(self)
35186, ss167380896, ss825373956, ss1585330934, ss1712390304, ss3642810417, ss3847357294	NC_000001.9:187665260:T:G	NC_000001.11:189429507:T:G	(self)
4718871, 2588380, 1831972, 1126830, 979268, 66556, 1214517, 2521697, 647087, 5537135, 2588380, 556653, ss218782030, ss230827071, ss536752796, ss554970967, ss832715291, ss975937837, ss1068455991, ss1293892356, ss1601730510, ss1644724543, ss1919172587, ss2020103287, ss2094988676, ss2148130733, ss2764053117, ss2988140281, ss3343823239, ss3626265967, ss3637802727, ss3651501407, ss3656093724, ss3727694403, ss3747102727, ss3850504717, ss3984840629, ss4016951848, ss5147567828, ss5323581732, ss5506119258, ss5627069988, ss5832996194, ss5938889778	NC_000001.10:189398637:T:G	NC_000001.11:189429507:T:G	(self)
6412820, 34021026, 226881, 8915683, 40436351, 13635512058, ss2168524622, ss3688251575, ss3800106578, ss4476830016, ss5245131843, ss5445632747, ss5518886885, ss5675078579, ss5911211711	NC_000001.11:189429507:T:G	NC_000001.11:189429507:T:G	(self)
ss66734066, ss66980567, ss67153024, ss70404682, ss70554758, ss71091462, ss75690616, ss85180638, ss121534640, ss153127336, ss159202844, ss170039730, ss171840195	NT_004487.19:40887279:T:G	NC_000001.11:189429507:T:G	(self)
ss18178338	NT_004671.15:753623:T:G	NC_000001.11:189429507:T:G	(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 rs12079586

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

rs12079586