Name: rs12374406
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.

rs12374406

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:99269867 (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=0.270414 (71576/264690, TOPMED)
T=0.257668 (36071/139990, GnomAD)
C=0.17503 (4946/28258, 14KJPN) (+ 15 more)
T=0.25246 (4769/18890, ALFA)
C=0.17297 (2899/16760, 8.3KJPN)
T=0.3865 (2475/6404, 1000G_30x)
T=0.4004 (2005/5008, 1000G)
T=0.2324 (1041/4480, Estonian)
T=0.2465 (950/3854, ALSPAC)
T=0.2344 (869/3708, TWINSUK)
C=0.2007 (588/2930, KOREAN)
C=0.1889 (346/1832, Korea1K)
T=0.236 (236/998, GoNL)
T=0.190 (114/600, NorthernSweden)
C=0.345 (96/278, SGDP_PRJ)
T=0.264 (57/216, Qatari)
C=0.162 (35/216, Vietnamese)
C=0.44 (7/16, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC100507053 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18890	C=0.74754	T=0.25246	0.558179	0.063102	0.378719	0
European	Sub	14286	C=0.75815	T=0.24185	0.570489	0.054179	0.375332	3
African	Sub	2946	C=0.7213	T=0.2787	0.517312	0.074678	0.408011	0
African Others	Sub	114	C=0.754	T=0.246	0.596491	0.087719	0.315789	1
African American	Sub	2832	C=0.7200	T=0.2800	0.514124	0.074153	0.411723	0
Asian	Sub	112	C=0.170	T=0.830	0.017857	0.678571	0.303571	0
East Asian	Sub	86	C=0.16	T=0.84	0.0	0.674419	0.325581	1
Other Asian	Sub	26	C=0.19	T=0.81	0.076923	0.692308	0.230769	1
Latin American 1	Sub	146	C=0.705	T=0.295	0.520548	0.109589	0.369863	1
Latin American 2	Sub	610	C=0.808	T=0.192	0.652459	0.036066	0.311475	0
South Asian	Sub	98	C=0.51	T=0.49	0.22449	0.204082	0.571429	1
Other	Sub	692	C=0.723	T=0.277	0.537572	0.092486	0.369942	1

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=0.729586	T=0.270414
gnomAD - Genomes	Global	Study-wide	139990	C=0.742332	T=0.257668
gnomAD - Genomes	European	Sub	75820	C=0.76816	T=0.23184
gnomAD - Genomes	African	Sub	41940	C=0.71767	T=0.28233
gnomAD - Genomes	American	Sub	13630	C=0.80088	T=0.19912
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.7517	T=0.2483
gnomAD - Genomes	East Asian	Sub	3128	C=0.1957	T=0.8043
gnomAD - Genomes	Other	Sub	2150	C=0.7223	T=0.2777
14KJPN	JAPANESE	Study-wide	28258	C=0.17503	T=0.82497
Allele Frequency Aggregator	Total	Global	18890	C=0.74754	T=0.25246
Allele Frequency Aggregator	European	Sub	14286	C=0.75815	T=0.24185
Allele Frequency Aggregator	African	Sub	2946	C=0.7213	T=0.2787
Allele Frequency Aggregator	Other	Sub	692	C=0.723	T=0.277
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.808	T=0.192
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.705	T=0.295
Allele Frequency Aggregator	Asian	Sub	112	C=0.170	T=0.830
Allele Frequency Aggregator	South Asian	Sub	98	C=0.51	T=0.49
8.3KJPN	JAPANESE	Study-wide	16760	C=0.17297	T=0.82703
1000Genomes_30x	Global	Study-wide	6404	C=0.6135	T=0.3865
1000Genomes_30x	African	Sub	1786	C=0.7497	T=0.2503
1000Genomes_30x	Europe	Sub	1266	C=0.7370	T=0.2630
1000Genomes_30x	South Asian	Sub	1202	C=0.5000	T=0.5000
1000Genomes_30x	East Asian	Sub	1170	C=0.2068	T=0.7932
1000Genomes_30x	American	Sub	980	C=0.831	T=0.169
1000Genomes	Global	Study-wide	5008	C=0.5996	T=0.4004
1000Genomes	African	Sub	1322	C=0.7496	T=0.2504
1000Genomes	East Asian	Sub	1008	C=0.2014	T=0.7986
1000Genomes	Europe	Sub	1006	C=0.7455	T=0.2545
1000Genomes	South Asian	Sub	978	C=0.501	T=0.499
1000Genomes	American	Sub	694	C=0.820	T=0.180
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.7676	T=0.2324
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.7535	T=0.2465
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.7656	T=0.2344
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.2007	T=0.7993
Korean Genome Project	KOREAN	Study-wide	1832	C=0.1889	T=0.8111
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.764	T=0.236
Northern Sweden	ACPOP	Study-wide	600	C=0.810	T=0.190
SGDP_PRJ	Global	Study-wide	278	C=0.345	T=0.655
Qatari	Global	Study-wide	216	C=0.736	T=0.264
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.162	T=0.838
Siberian	Global	Study-wide	16	C=0.44	T=0.56

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 4	NC_000004.12:g.99269867C>T
GRCh37.p13 chr 4	NC_000004.11:g.100191024C>T

Gene: LOC100507053, uncharacterized LOC100507053 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100507053 transcript	NR_037884.1:n.	N/A	Intron 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=	T
GRCh38.p14 chr 4	NC_000004.12:g.99269867=	NC_000004.12:g.99269867C>T
GRCh37.p13 chr 4	NC_000004.11:g.100191024=	NC_000004.11:g.100191024C>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#.

51 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss19012818	Feb 28, 2004 (120)
2	ABI	ss42283764	Mar 14, 2006 (126)
3	HGSV	ss85959890	Dec 14, 2007 (130)
4	BCMHGSC_JDW	ss92703332	Mar 24, 2008 (129)
5	HUMANGENOME_JCVI	ss98986829	Feb 04, 2009 (130)
6	ENSEMBL	ss139478299	Dec 01, 2009 (131)
7	ENSEMBL	ss139782228	Dec 01, 2009 (131)
8	GMI	ss157650821	Dec 01, 2009 (131)
9	GMI	ss277844460	May 04, 2012 (137)
10	GMI	ss284967897	Apr 25, 2013 (138)
11	PJP	ss293147538	May 09, 2011 (134)
12	1000GENOMES	ss331832225	May 09, 2011 (134)
13	SSMP	ss651525787	Apr 25, 2013 (138)
14	EVA-GONL	ss980450332	Aug 21, 2014 (142)
15	JMKIDD_LAB	ss1071787261	Aug 21, 2014 (142)
16	1000GENOMES	ss1310980551	Aug 21, 2014 (142)
17	EVA_DECODE	ss1589954363	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1610736683	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1653730716	Apr 01, 2015 (144)
20	WEILL_CORNELL_DGM	ss1923690369	Feb 12, 2016 (147)
21	JJLAB	ss2022431153	Sep 14, 2016 (149)
22	USC_VALOUEV	ss2150560327	Dec 20, 2016 (150)
23	HUMAN_LONGEVITY	ss2265426778	Dec 20, 2016 (150)
24	SYSTEMSBIOZJU	ss2625714514	Nov 08, 2017 (151)
25	GRF	ss2706037155	Nov 08, 2017 (151)
26	GNOMAD	ss2812856630	Nov 08, 2017 (151)
27	SWEGEN	ss2995210819	Nov 08, 2017 (151)
28	CSHL	ss3345861906	Nov 08, 2017 (151)
29	BIOINF_KMB_FNS_UNIBA	ss3645814306	Oct 12, 2018 (152)
30	URBANLAB	ss3647802689	Oct 12, 2018 (152)
31	EGCUT_WGS	ss3663106669	Jul 13, 2019 (153)
32	EVA_DECODE	ss3712657193	Jul 13, 2019 (153)
33	ACPOP	ss3731421987	Jul 13, 2019 (153)
34	EVA	ss3762167263	Jul 13, 2019 (153)
35	KHV_HUMAN_GENOMES	ss3805315692	Jul 13, 2019 (153)
36	EVA	ss3828703652	Apr 26, 2020 (154)
37	SGDP_PRJ	ss3859611005	Apr 26, 2020 (154)
38	KRGDB	ss3905888552	Apr 26, 2020 (154)
39	KOGIC	ss3954742598	Apr 26, 2020 (154)
40	TOPMED	ss4624647187	Apr 26, 2021 (155)
41	TOMMO_GENOMICS	ss5167079227	Apr 26, 2021 (155)
42	1000G_HIGH_COVERAGE	ss5260289118	Oct 13, 2022 (156)
43	EVA	ss5350977504	Oct 13, 2022 (156)
44	EVA	ss5507641584	Oct 13, 2022 (156)
45	1000G_HIGH_COVERAGE	ss5541957353	Oct 13, 2022 (156)
46	SANFORD_IMAGENETICS	ss5635665971	Oct 13, 2022 (156)
47	TOMMO_GENOMICS	ss5701810707	Oct 13, 2022 (156)
48	YY_MCH	ss5805354142	Oct 13, 2022 (156)
49	EVA	ss5844424499	Oct 13, 2022 (156)
50	EVA	ss5864677798	Oct 13, 2022 (156)
51	EVA	ss5964056688	Oct 13, 2022 (156)
52	1000Genomes	NC_000004.11 - 100191024	Oct 12, 2018 (152)
53	1000Genomes_30x	NC_000004.12 - 99269867	Oct 13, 2022 (156)
54	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 100191024	Oct 12, 2018 (152)
55	Genetic variation in the Estonian population	NC_000004.11 - 100191024	Oct 12, 2018 (152)
56	gnomAD - Genomes	NC_000004.12 - 99269867	Apr 26, 2021 (155)
57	Genome of the Netherlands Release 5	NC_000004.11 - 100191024	Apr 26, 2020 (154)
58	KOREAN population from KRGDB	NC_000004.11 - 100191024	Apr 26, 2020 (154)
59	Korean Genome Project	NC_000004.12 - 99269867	Apr 26, 2020 (154)
60	Northern Sweden	NC_000004.11 - 100191024	Jul 13, 2019 (153)
61	Qatari	NC_000004.11 - 100191024	Apr 26, 2020 (154)
62	SGDP_PRJ	NC_000004.11 - 100191024	Apr 26, 2020 (154)
63	Siberian	NC_000004.11 - 100191024	Apr 26, 2020 (154)
64	8.3KJPN	NC_000004.11 - 100191024	Apr 26, 2021 (155)
65	14KJPN	NC_000004.12 - 99269867	Oct 13, 2022 (156)
66	TopMed	NC_000004.12 - 99269867	Apr 26, 2021 (155)
67	UK 10K study - Twins	NC_000004.11 - 100191024	Oct 12, 2018 (152)
68	A Vietnamese Genetic Variation Database	NC_000004.11 - 100191024	Jul 13, 2019 (153)
69	ALFA	NC_000004.12 - 99269867	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).

Associated ID	History Updated (Build)
rs57837747	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss85959890	NC_000004.9:100548201:C:T	NC_000004.12:99269866:C:T	(self)
ss92703332, ss277844460, ss284967897, ss293147538, ss1589954363	NC_000004.10:100410046:C:T	NC_000004.12:99269866:C:T	(self)
22422771, 12472938, 8844917, 5513814, 13065946, 4706852, 5732299, 11627985, 3076681, 25048534, 12472938, 2744419, ss331832225, ss651525787, ss980450332, ss1071787261, ss1310980551, ss1610736683, ss1653730716, ss1923690369, ss2022431153, ss2150560327, ss2625714514, ss2706037155, ss2812856630, ss2995210819, ss3345861906, ss3663106669, ss3731421987, ss3762167263, ss3828703652, ss3859611005, ss3905888552, ss5167079227, ss5350977504, ss5507641584, ss5635665971, ss5844424499, ss5964056688	NC_000004.11:100191023:C:T	NC_000004.12:99269866:C:T	(self)
29483288, 158839243, 11120599, 35647811, 462024743, 9003577320, ss2265426778, ss3645814306, ss3647802689, ss3712657193, ss3805315692, ss3954742598, ss4624647187, ss5260289118, ss5541957353, ss5701810707, ss5805354142, ss5864677798	NC_000004.12:99269866:C:T	NC_000004.12:99269866:C:T	(self)
ss19012818	NT_016354.16:24685727:C:T	NC_000004.12:99269866:C:T	(self)
ss42283764, ss98986829, ss139478299, ss139782228, ss157650821	NT_016354.19:24738744:C:T	NC_000004.12:99269866: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 rs12374406

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

rs12374406