Name: rs13386112
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.

rs13386112

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:21243 (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=0.091352 (24180/264690, TOPMED)
T=0.088760 (12442/140176, GnomAD)
T=0.02828 (799/28258, 14KJPN) (+ 14 more)
T=0.05818 (1099/18890, ALFA)
T=0.02876 (482/16760, 8.3KJPN)
T=0.1062 (680/6404, 1000G_30x)
T=0.1046 (524/5008, 1000G)
T=0.0257 (99/3854, ALSPAC)
T=0.0254 (94/3708, TWINSUK)
T=0.0440 (129/2930, KOREAN)
T=0.0486 (89/1832, Korea1K)
T=0.030 (30/998, GoNL)
T=0.060 (36/600, NorthernSweden)
T=0.082 (27/328, HapMap)
T=0.074 (16/216, Qatari)
T=0.070 (15/214, Vietnamese)
C=0.35 (32/92, 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	18890	C=0.94182	T=0.05818
European	Sub	14286	C=0.96927	T=0.03073
African	Sub	2946	C=0.8041	T=0.1959
African Others	Sub	114	C=0.816	T=0.184
African American	Sub	2832	C=0.8037	T=0.1963
Asian	Sub	112	C=0.938	T=0.062
East Asian	Sub	86	C=0.94	T=0.06
Other Asian	Sub	26	C=0.92	T=0.08
Latin American 1	Sub	146	C=0.897	T=0.103
Latin American 2	Sub	610	C=0.977	T=0.023
South Asian	Sub	98	C=0.99	T=0.01
Other	Sub	692	C=0.934	T=0.066

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=0.908648	T=0.091352
gnomAD - Genomes	Global	Study-wide	140176	C=0.911240	T=0.088760
gnomAD - Genomes	European	Sub	75948	C=0.97223	T=0.02777
gnomAD - Genomes	African	Sub	41970	C=0.78551	T=0.21449
gnomAD - Genomes	American	Sub	13660	C=0.95264	T=0.04736
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.9063	T=0.0937
gnomAD - Genomes	East Asian	Sub	3132	C=0.9352	T=0.0648
gnomAD - Genomes	Other	Sub	2146	C=0.9208	T=0.0792
14KJPN	JAPANESE	Study-wide	28258	C=0.97172	T=0.02828
Allele Frequency Aggregator	Total	Global	18890	C=0.94182	T=0.05818
Allele Frequency Aggregator	European	Sub	14286	C=0.96927	T=0.03073
Allele Frequency Aggregator	African	Sub	2946	C=0.8041	T=0.1959
Allele Frequency Aggregator	Other	Sub	692	C=0.934	T=0.066
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.977	T=0.023
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.897	T=0.103
Allele Frequency Aggregator	Asian	Sub	112	C=0.938	T=0.062
Allele Frequency Aggregator	South Asian	Sub	98	C=0.99	T=0.01
8.3KJPN	JAPANESE	Study-wide	16760	C=0.97124	T=0.02876
1000Genomes_30x	Global	Study-wide	6404	C=0.8938	T=0.1062
1000Genomes_30x	African	Sub	1786	C=0.7363	T=0.2637
1000Genomes_30x	Europe	Sub	1266	C=0.9652	T=0.0348
1000Genomes_30x	South Asian	Sub	1202	C=0.9542	T=0.0458
1000Genomes_30x	East Asian	Sub	1170	C=0.9573	T=0.0427
1000Genomes_30x	American	Sub	980	C=0.939	T=0.061
1000Genomes	Global	Study-wide	5008	C=0.8954	T=0.1046
1000Genomes	African	Sub	1322	C=0.7284	T=0.2716
1000Genomes	East Asian	Sub	1008	C=0.9623	T=0.0377
1000Genomes	Europe	Sub	1006	C=0.9642	T=0.0358
1000Genomes	South Asian	Sub	978	C=0.951	T=0.049
1000Genomes	American	Sub	694	C=0.938	T=0.062
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9743	T=0.0257
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9746	T=0.0254
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.9560	T=0.0440
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9514	T=0.0486
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.970	T=0.030
Northern Sweden	ACPOP	Study-wide	600	C=0.940	T=0.060
HapMap	Global	Study-wide	328	C=0.918	T=0.082
HapMap	American	Sub	120	C=0.983	T=0.017
HapMap	African	Sub	118	C=0.797	T=0.203
HapMap	Asian	Sub	90	C=0.99	T=0.01
Qatari	Global	Study-wide	216	C=0.926	T=0.074
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.930	T=0.070
SGDP_PRJ	Global	Study-wide	92	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 2	NC_000002.12:g.21243C>T
GRCh37.p13 chr 2	NC_000002.11:g.21243C>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 2	NC_000002.12:g.21243=	NC_000002.12:g.21243C>T
GRCh37.p13 chr 2	NC_000002.11:g.21243=	NC_000002.11:g.21243C>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#.

42 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WUGSC_SSAHASNP	ss23058065	Apr 05, 2004 (121)
2	1000GENOMES	ss112137816	Jan 25, 2009 (130)
3	ILLUMINA-UK	ss117555072	Feb 14, 2009 (130)
4	COMPLETE_GENOMICS	ss162981138	Jul 04, 2010 (132)
5	BUSHMAN	ss199922925	Jul 04, 2010 (132)
6	1000GENOMES	ss219013229	Jul 14, 2010 (132)
7	TISHKOFF	ss555295642	Apr 25, 2013 (138)
8	SSMP	ss648872607	Apr 25, 2013 (138)
9	EVA-GONL	ss976396834	Aug 21, 2014 (142)
10	JMKIDD_LAB	ss1068790766	Aug 21, 2014 (142)
11	1000GENOMES	ss1295574511	Aug 21, 2014 (142)
12	EVA_DECODE	ss1585798233	Apr 01, 2015 (144)
13	EVA_UK10K_ALSPAC	ss1602626840	Apr 01, 2015 (144)
14	EVA_UK10K_TWINSUK	ss1645620873	Apr 01, 2015 (144)
15	HAMMER_LAB	ss1796107800	Sep 08, 2015 (146)
16	WEILL_CORNELL_DGM	ss1919623837	Feb 12, 2016 (147)
17	JJLAB	ss2020339327	Sep 14, 2016 (149)
18	GRF	ss2702930161	Nov 08, 2017 (151)
19	GNOMAD	ss2768814914	Nov 08, 2017 (151)
20	SWEGEN	ss2988841623	Nov 08, 2017 (151)
21	CSHL	ss3344030029	Nov 08, 2017 (151)
22	EVA_DECODE	ss3703083909	Jul 12, 2019 (153)
23	ACPOP	ss3728076148	Jul 12, 2019 (153)
24	EVA	ss3756245612	Jul 12, 2019 (153)
25	KHV_HUMAN_GENOMES	ss3800634330	Jul 12, 2019 (153)
26	SGDP_PRJ	ss3851402833	Apr 25, 2020 (154)
27	KRGDB	ss3896770491	Apr 25, 2020 (154)
28	KOGIC	ss3946946653	Apr 25, 2020 (154)
29	TOPMED	ss4491456347	Apr 25, 2021 (155)
30	TOMMO_GENOMICS	ss5149497041	Apr 25, 2021 (155)
31	1000G_HIGH_COVERAGE	ss5246618168	Oct 12, 2022 (156)
32	EVA	ss5326259229	Oct 12, 2022 (156)
33	HUGCELL_USP	ss5446965086	Oct 12, 2022 (156)
34	EVA	ss5506268407	Oct 12, 2022 (156)
35	1000G_HIGH_COVERAGE	ss5521110260	Oct 12, 2022 (156)
36	SANFORD_IMAGENETICS	ss5627923501	Oct 12, 2022 (156)
37	TOMMO_GENOMICS	ss5677567537	Oct 12, 2022 (156)
38	YY_MCH	ss5801853350	Oct 12, 2022 (156)
39	EVA	ss5819540880	Oct 12, 2022 (156)
40	EVA	ss5852352027	Oct 12, 2022 (156)
41	EVA	ss5928688470	Oct 12, 2022 (156)
42	EVA	ss5954107693	Oct 12, 2022 (156)
43	1000Genomes	NC_000002.11 - 21243	Oct 11, 2018 (152)
44	1000Genomes_30x	NC_000002.12 - 21243	Oct 12, 2022 (156)
45	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 21243	Oct 11, 2018 (152)
46	gnomAD - Genomes	NC_000002.12 - 21243	Apr 25, 2021 (155)
47	Genome of the Netherlands Release 5	NC_000002.11 - 21243	Apr 25, 2020 (154)
48	HapMap	NC_000002.12 - 21243	Apr 25, 2020 (154)
49	KOREAN population from KRGDB	NC_000002.11 - 21243	Apr 25, 2020 (154)
50	Korean Genome Project	NC_000002.12 - 21243	Apr 25, 2020 (154)
51	Northern Sweden	NC_000002.11 - 21243	Jul 12, 2019 (153)
52	Qatari	NC_000002.11 - 21243	Apr 25, 2020 (154)
53	SGDP_PRJ	NC_000002.11 - 21243	Apr 25, 2020 (154)
54	8.3KJPN	NC_000002.11 - 21243	Apr 25, 2021 (155)
55	14KJPN	NC_000002.12 - 21243	Oct 12, 2022 (156)
56	TopMed	NC_000002.12 - 21243	Apr 25, 2021 (155)
57	UK 10K study - Twins	NC_000002.11 - 21243	Oct 11, 2018 (152)
58	A Vietnamese Genetic Variation Database	NC_000002.11 - 21243	Jul 12, 2019 (153)
59	ALFA	NC_000002.12 - 21243	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
ss112137816, ss117555072, ss162981138, ss199922925, ss1585798233	NC_000002.10:11242:C:T	NC_000002.12:21242:C:T	(self)
6464387, 3576926, 1572282, 3947885, 1361013, 1665767, 3419813, 7466348, 3576926, 780715, ss219013229, ss555295642, ss648872607, ss976396834, ss1068790766, ss1295574511, ss1602626840, ss1645620873, ss1796107800, ss1919623837, ss2020339327, ss2702930161, ss2768814914, ss2988841623, ss3344030029, ss3728076148, ss3756245612, ss3851402833, ss3896770491, ss5149497041, ss5326259229, ss5506268407, ss5627923501, ss5819540880, ss5954107693	NC_000002.11:21242:C:T	NC_000002.12:21242:C:T	(self)
8636195, 46150530, 1718362, 3324654, 11404641, 295279226, 609202678, ss3703083909, ss3800634330, ss3946946653, ss4491456347, ss5246618168, ss5446965086, ss5521110260, ss5677567537, ss5801853350, ss5852352027, ss5928688470	NC_000002.12:21242:C:T	NC_000002.12:21242:C:T	(self)
ss23058065	NT_022327.13:11242:C:T	NC_000002.12:21242: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 rs13386112

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

rs13386112