Name: rs12728322
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.

rs12728322

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:92829235 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.264770 (70082/264690, TOPMED)
T=0.272695 (38077/139632, GnomAD)
T=0.26183 (16308/62284, ALFA) (+ 20 more)
T=0.00881 (249/28256, 14KJPN)
T=0.00883 (148/16760, 8.3KJPN)
T=0.2114 (1354/6404, 1000G_30x)
T=0.2079 (1041/5008, 1000G)
T=0.2310 (1034/4476, Estonian)
T=0.2670 (1029/3854, ALSPAC)
T=0.2762 (1024/3708, TWINSUK)
T=0.0157 (46/2922, KOREAN)
T=0.2039 (425/2084, HGDP_Stanford)
T=0.2283 (432/1892, HapMap)
T=0.0076 (14/1832, Korea1K)
T=0.2042 (232/1136, Daghestan)
T=0.252 (251/998, GoNL)
T=0.242 (145/600, NorthernSweden)
T=0.264 (57/216, Qatari)
T=0.019 (4/212, Vietnamese)
C=0.406 (73/180, SGDP_PRJ)
T=0.25 (10/40, GENOME_DK)
T=0.29 (10/34, Ancient Sardinia)
C=0.39 (11/28, Siberian)

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	62284	C=0.73817	T=0.26183
European	Sub	43762	C=0.73447	T=0.26553
African	Sub	7798	C=0.6854	T=0.3146
African Others	Sub	274	C=0.690	T=0.310
African American	Sub	7524	C=0.6853	T=0.3147
Asian	Sub	456	C=0.989	T=0.011
East Asian	Sub	388	C=0.992	T=0.008
Other Asian	Sub	68	C=0.97	T=0.03
Latin American 1	Sub	596	C=0.706	T=0.294
Latin American 2	Sub	4994	C=0.8120	T=0.1880
South Asian	Sub	180	C=0.822	T=0.178
Other	Sub	4498	C=0.7590	T=0.2410

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.735230	T=0.264770
gnomAD - Genomes	Global	Study-wide	139632	C=0.727305	T=0.272695
gnomAD - Genomes	European	Sub	75680	C=0.73439	T=0.26561
gnomAD - Genomes	African	Sub	41762	C=0.68438	T=0.31562
gnomAD - Genomes	American	Sub	13596	C=0.74375	T=0.25625
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.7935	T=0.2065
gnomAD - Genomes	East Asian	Sub	3128	C=0.9837	T=0.0163
gnomAD - Genomes	Other	Sub	2144	C=0.7323	T=0.2677
Allele Frequency Aggregator	Total	Global	62284	C=0.73817	T=0.26183
Allele Frequency Aggregator	European	Sub	43762	C=0.73447	T=0.26553
Allele Frequency Aggregator	African	Sub	7798	C=0.6854	T=0.3146
Allele Frequency Aggregator	Latin American 2	Sub	4994	C=0.8120	T=0.1880
Allele Frequency Aggregator	Other	Sub	4498	C=0.7590	T=0.2410
Allele Frequency Aggregator	Latin American 1	Sub	596	C=0.706	T=0.294
Allele Frequency Aggregator	Asian	Sub	456	C=0.989	T=0.011
Allele Frequency Aggregator	South Asian	Sub	180	C=0.822	T=0.178
14KJPN	JAPANESE	Study-wide	28256	C=0.99119	T=0.00881
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99117	T=0.00883
1000Genomes_30x	Global	Study-wide	6404	C=0.7886	T=0.2114
1000Genomes_30x	African	Sub	1786	C=0.6797	T=0.3203
1000Genomes_30x	Europe	Sub	1266	C=0.7243	T=0.2757
1000Genomes_30x	South Asian	Sub	1202	C=0.8186	T=0.1814
1000Genomes_30x	East Asian	Sub	1170	C=0.9880	T=0.0120
1000Genomes_30x	American	Sub	980	C=0.795	T=0.205
1000Genomes	Global	Study-wide	5008	C=0.7921	T=0.2079
1000Genomes	African	Sub	1322	C=0.6762	T=0.3238
1000Genomes	East Asian	Sub	1008	C=0.9891	T=0.0109
1000Genomes	Europe	Sub	1006	C=0.7256	T=0.2744
1000Genomes	South Asian	Sub	978	C=0.822	T=0.178
1000Genomes	American	Sub	694	C=0.781	T=0.219
Genetic variation in the Estonian population	Estonian	Study-wide	4476	C=0.7690	T=0.2310
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7330	T=0.2670
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7238	T=0.2762
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9843	T=0.0157
HGDP-CEPH-db Supplement 1	Global	Study-wide	2084	C=0.7961	T=0.2039
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	C=0.962	T=0.038
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	C=0.829	T=0.171
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	C=0.694	T=0.306
HGDP-CEPH-db Supplement 1	Europe	Sub	320	C=0.719	T=0.281
HGDP-CEPH-db Supplement 1	Africa	Sub	242	C=0.632	T=0.368
HGDP-CEPH-db Supplement 1	America	Sub	216	C=0.769	T=0.231
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	C=1.00	T=0.00
HapMap	Global	Study-wide	1892	C=0.7717	T=0.2283
HapMap	American	Sub	770	C=0.817	T=0.183
HapMap	African	Sub	692	C=0.645	T=0.355
HapMap	Asian	Sub	254	C=0.996	T=0.004
HapMap	Europe	Sub	176	C=0.750	T=0.250
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9924	T=0.0076
Genome-wide autozygosity in Daghestan	Global	Study-wide	1136	C=0.7958	T=0.2042
Genome-wide autozygosity in Daghestan	Daghestan	Sub	628	C=0.814	T=0.186
Genome-wide autozygosity in Daghestan	Near_East	Sub	144	C=0.736	T=0.264
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	C=0.762	T=0.238
Genome-wide autozygosity in Daghestan	Europe	Sub	108	C=0.787	T=0.213
Genome-wide autozygosity in Daghestan	South Asian	Sub	98	C=0.88	T=0.12
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	C=0.64	T=0.36
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.748	T=0.252
Northern Sweden	ACPOP	Study-wide	600	C=0.758	T=0.242
Qatari	Global	Study-wide	216	C=0.736	T=0.264
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.981	T=0.019
SGDP_PRJ	Global	Study-wide	180	C=0.406	T=0.594
The Danish reference pan genome	Danish	Study-wide	40	C=0.75	T=0.25
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	34	C=0.71	T=0.29
Siberian	Global	Study-wide	28	C=0.39	T=0.61

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.92829235C>T
GRCh37.p13 chr 1	NC_000001.10:g.93294792C>T
RPL5 RefSeqGene (LRG_1155)	NG_011779.2:g.2250C>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=	T
GRCh38.p14 chr 1	NC_000001.11:g.92829235=	NC_000001.11:g.92829235C>T
GRCh37.p13 chr 1	NC_000001.10:g.93294792=	NC_000001.10:g.93294792C>T
RPL5 RefSeqGene (LRG_1155)	NG_011779.2:g.2250=	NG_011779.2:g.2250C>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#.

85 SubSNP, 23 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss20456813	Apr 05, 2004 (121)
2	ILLUMINA	ss67360400	Dec 01, 2006 (127)
3	ILLUMINA	ss71125889	May 18, 2007 (127)
4	ILLUMINA	ss75384001	Dec 06, 2007 (129)
5	1000GENOMES	ss108416025	Jan 23, 2009 (130)
6	1000GENOMES	ss110828348	Jan 25, 2009 (130)
7	KRIBB_YJKIM	ss119808766	Dec 01, 2009 (131)
8	ENSEMBL	ss131825629	Dec 01, 2009 (131)
9	ILLUMINA	ss160297262	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss163667671	Jul 04, 2010 (132)
11	COMPLETE_GENOMICS	ss164793498	Jul 04, 2010 (132)
12	BUSHMAN	ss198780067	Jul 04, 2010 (132)
13	1000GENOMES	ss218525575	Jul 14, 2010 (132)
14	1000GENOMES	ss230638676	Jul 14, 2010 (132)
15	ILLUMINA	ss480405805	Sep 08, 2015 (146)
16	ILLUMINA	ss482434916	May 04, 2012 (137)
17	ILLUMINA	ss484297037	May 04, 2012 (137)
18	ILLUMINA	ss536481133	Sep 08, 2015 (146)
19	TISHKOFF	ss554432963	Apr 25, 2013 (138)
20	SSMP	ss648222287	Apr 25, 2013 (138)
21	ILLUMINA	ss779446516	Sep 08, 2015 (146)
22	ILLUMINA	ss782594655	Sep 08, 2015 (146)
23	ILLUMINA	ss834916013	Sep 08, 2015 (146)
24	EVA-GONL	ss975434352	Aug 21, 2014 (142)
25	JMKIDD_LAB	ss1068092995	Aug 21, 2014 (142)
26	1000GENOMES	ss1291925916	Aug 21, 2014 (142)
27	HAMMER_LAB	ss1397253846	Sep 08, 2015 (146)
28	DDI	ss1425897749	Apr 01, 2015 (144)
29	EVA_GENOME_DK	ss1574234762	Apr 01, 2015 (144)
30	EVA_DECODE	ss1584810598	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1600717775	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1643711808	Apr 01, 2015 (144)
33	EVA_SVP	ss1712353488	Apr 01, 2015 (144)
34	HAMMER_LAB	ss1794744389	Sep 08, 2015 (146)
35	WEILL_CORNELL_DGM	ss1918635242	Feb 12, 2016 (147)
36	GENOMED	ss1966809579	Jul 19, 2016 (147)
37	JJLAB	ss2019839233	Sep 14, 2016 (149)
38	ILLUMINA	ss2094845012	Dec 20, 2016 (150)
39	ILLUMINA	ss2094967253	Dec 20, 2016 (150)
40	USC_VALOUEV	ss2147857203	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2164640302	Dec 20, 2016 (150)
42	SYSTEMSBIOZJU	ss2624430995	Nov 08, 2017 (151)
43	ILLUMINA	ss2632547862	Nov 08, 2017 (151)
44	ILLUMINA	ss2635001110	Nov 08, 2017 (151)
45	GRF	ss2697783023	Nov 08, 2017 (151)
46	GNOMAD	ss2758108636	Nov 08, 2017 (151)
47	SWEGEN	ss2987232532	Nov 08, 2017 (151)
48	BIOINF_KMB_FNS_UNIBA	ss3023682404	Nov 08, 2017 (151)
49	CSHL	ss3343575064	Nov 08, 2017 (151)
50	ILLUMINA	ss3626155158	Oct 11, 2018 (152)
51	ILLUMINA	ss3630582331	Oct 11, 2018 (152)
52	ILLUMINA	ss3636014085	Oct 11, 2018 (152)
53	ILLUMINA	ss3642782821	Oct 11, 2018 (152)
54	URBANLAB	ss3646721078	Oct 11, 2018 (152)
55	ILLUMINA	ss3651440220	Oct 11, 2018 (152)
56	EGCUT_WGS	ss3655311109	Jul 12, 2019 (153)
57	EVA_DECODE	ss3687277908	Jul 12, 2019 (153)
58	ACPOP	ss3727274037	Jul 12, 2019 (153)
59	EVA	ss3746518427	Jul 12, 2019 (153)
60	PACBIO	ss3783483733	Jul 12, 2019 (153)
61	PACBIO	ss3789130749	Jul 12, 2019 (153)
62	PACBIO	ss3794003567	Jul 12, 2019 (153)
63	KHV_HUMAN_GENOMES	ss3799522529	Jul 12, 2019 (153)
64	EVA	ss3826304164	Apr 25, 2020 (154)
65	EVA	ss3836542521	Apr 25, 2020 (154)
66	EVA	ss3841950239	Apr 25, 2020 (154)
67	HGDP	ss3847342326	Apr 25, 2020 (154)
68	SGDP_PRJ	ss3849384936	Apr 25, 2020 (154)
69	KRGDB	ss3894451488	Apr 25, 2020 (154)
70	KOGIC	ss3945004841	Apr 25, 2020 (154)
71	EVA	ss3984812362	Apr 25, 2021 (155)
72	TOPMED	ss4459016340	Apr 25, 2021 (155)
73	TOMMO_GENOMICS	ss5145107309	Apr 25, 2021 (155)
74	1000G_HIGH_COVERAGE	ss5243166236	Oct 12, 2022 (156)
75	EVA	ss5314634667	Oct 12, 2022 (156)
76	HUGCELL_USP	ss5444133187	Oct 12, 2022 (156)
77	EVA	ss5505948080	Oct 12, 2022 (156)
78	1000G_HIGH_COVERAGE	ss5515920924	Oct 12, 2022 (156)
79	SANFORD_IMAGENETICS	ss5626044515	Oct 12, 2022 (156)
80	TOMMO_GENOMICS	ss5670208404	Oct 12, 2022 (156)
81	YY_MCH	ss5800821236	Oct 12, 2022 (156)
82	EVA	ss5832309555	Oct 12, 2022 (156)
83	EVA	ss5849015085	Oct 12, 2022 (156)
84	EVA	ss5909291522	Oct 12, 2022 (156)
85	EVA	ss5937898641	Oct 12, 2022 (156)
86	1000Genomes	NC_000001.10 - 93294792	Oct 11, 2018 (152)
87	1000Genomes_30x	NC_000001.11 - 92829235	Oct 12, 2022 (156)
88	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 93294792	Oct 11, 2018 (152)
89	Genome-wide autozygosity in Daghestan	NC_000001.9 - 93067380	Apr 25, 2020 (154)
90	Genetic variation in the Estonian population	NC_000001.10 - 93294792	Oct 11, 2018 (152)
91	The Danish reference pan genome	NC_000001.10 - 93294792	Apr 25, 2020 (154)
92	gnomAD - Genomes	NC_000001.11 - 92829235	Apr 25, 2021 (155)
93	Genome of the Netherlands Release 5	NC_000001.10 - 93294792	Apr 25, 2020 (154)
94	HGDP-CEPH-db Supplement 1	NC_000001.9 - 93067380	Apr 25, 2020 (154)
95	HapMap	NC_000001.11 - 92829235	Apr 25, 2020 (154)
96	KOREAN population from KRGDB	NC_000001.10 - 93294792	Apr 25, 2020 (154)
97	Korean Genome Project	NC_000001.11 - 92829235	Apr 25, 2020 (154)
98	Northern Sweden	NC_000001.10 - 93294792	Jul 12, 2019 (153)
99	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000001.10 - 93294792	Apr 25, 2021 (155)
100	Qatari	NC_000001.10 - 93294792	Apr 25, 2020 (154)
101	SGDP_PRJ	NC_000001.10 - 93294792	Apr 25, 2020 (154)
102	Siberian	NC_000001.10 - 93294792	Apr 25, 2020 (154)
103	8.3KJPN	NC_000001.10 - 93294792	Apr 25, 2021 (155)
104	14KJPN	NC_000001.11 - 92829235	Oct 12, 2022 (156)
105	TopMed	NC_000001.11 - 92829235	Apr 25, 2021 (155)
106	UK 10K study - Twins	NC_000001.10 - 93294792	Oct 11, 2018 (152)
107	A Vietnamese Genetic Variation Database	NC_000001.10 - 93294792	Jul 12, 2019 (153)
108	ALFA	NC_000001.11 - 92829235	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
15162, 20218, ss108416025, ss110828348, ss163667671, ss164793498, ss198780067, ss482434916, ss1397253846, ss1584810598, ss1712353488, ss2094845012, ss2635001110, ss3642782821, ss3847342326	NC_000001.9:93067379:C:T	NC_000001.11:92829234:C:T	(self)
2683000, 1475241, 1049357, 1609786, 639449, 1628882, 558902, 38289, 677172, 1401916, 373557, 3076616, 1475241, 317016, ss218525575, ss230638676, ss480405805, ss484297037, ss536481133, ss554432963, ss648222287, ss779446516, ss782594655, ss834916013, ss975434352, ss1068092995, ss1291925916, ss1425897749, ss1574234762, ss1600717775, ss1643711808, ss1794744389, ss1918635242, ss1966809579, ss2019839233, ss2094967253, ss2147857203, ss2624430995, ss2632547862, ss2697783023, ss2758108636, ss2987232532, ss3343575064, ss3626155158, ss3630582331, ss3636014085, ss3651440220, ss3655311109, ss3727274037, ss3746518427, ss3783483733, ss3789130749, ss3794003567, ss3826304164, ss3836542521, ss3849384936, ss3894451488, ss3984812362, ss5145107309, ss5314634667, ss5505948080, ss5626044515, ss5832309555, ss5937898641	NC_000001.10:93294791:C:T	NC_000001.11:92829234:C:T	(self)
3446859, 18938976, 127065, 1382842, 4045508, 22622675, 7734629319, ss2164640302, ss3023682404, ss3646721078, ss3687277908, ss3799522529, ss3841950239, ss3945004841, ss4459016340, ss5243166236, ss5444133187, ss5515920924, ss5670208404, ss5800821236, ss5849015085, ss5909291522	NC_000001.11:92829234:C:T	NC_000001.11:92829234:C:T	(self)
ss20456813	NT_028050.13:1492613:C:T	NC_000001.11:92829234:C:T	(self)
ss67360400, ss71125889, ss75384001, ss119808766, ss131825629, ss160297262	NT_032977.9:63266709:C:T	NC_000001.11:92829234: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 rs12728322

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs12728322