Name: rs13011424
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.

rs13011424

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:29053144 (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: G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.202309 (28352/140142, GnomAD)
T=0.00007 (2/28258, 14KJPN)
T=0.00006 (1/16760, 8.3KJPN) (+ 12 more)
T=0.09189 (1213/13200, ALFA)
T=0.1076 (689/6404, 1000G_30x)
T=0.1056 (529/5008, 1000G)
T=0.2511 (1125/4480, Estonian)
T=0.3025 (1166/3854, ALSPAC)
T=0.2824 (1047/3708, TWINSUK)
T=0.290 (289/998, GoNL)
T=0.278 (167/600, NorthernSweden)
T=0.255 (55/216, Qatari)
G=0.434 (46/106, SGDP_PRJ)
G=0.5 (5/10, Siberian)
T=0.5 (5/10, 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	13200	G=0.90811	C=0.00000, T=0.09189	0.836364	0.020152	0.143485	32
European	Sub	9330	G=0.8753	C=0.0000, T=0.1247	0.777921	0.027224	0.194855	28
African	Sub	2614	G=0.9985	C=0.0000, T=0.0015	0.99694	0.0	0.00306	0
African Others	Sub	114	G=1.000	C=0.000, T=0.000	1.0	0.0	0.0	N/A
African American	Sub	2500	G=0.9984	C=0.0000, T=0.0016	0.9968	0.0	0.0032	0
Asian	Sub	112	G=1.000	C=0.000, T=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	86	G=1.00	C=0.00, T=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	26	G=1.00	C=0.00, T=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	98	G=1.00	C=0.00, T=0.00	1.0	0.0	0.0	N/A
Latin American 2	Sub	450	G=1.000	C=0.000, T=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	68	G=1.00	C=0.00, T=0.00	1.0	0.0	0.0	N/A
Other	Sub	528	G=0.913	C=0.000, T=0.087	0.848485	0.022727	0.128788	6

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
gnomAD - Genomes	Global	Study-wide	140142	G=0.797691	T=0.202309
gnomAD - Genomes	European	Sub	75874	G=0.71540	T=0.28460
gnomAD - Genomes	African	Sub	42010	G=0.93961	T=0.06039
gnomAD - Genomes	American	Sub	13652	G=0.81519	T=0.18481
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	G=0.6325	T=0.3675
gnomAD - Genomes	East Asian	Sub	3132	G=0.9987	T=0.0013
gnomAD - Genomes	Other	Sub	2154	G=0.7799	T=0.2201
14KJPN	JAPANESE	Study-wide	28258	G=0.99993	T=0.00007
8.3KJPN	JAPANESE	Study-wide	16760	G=0.99994	T=0.00006
Allele Frequency Aggregator	Total	Global	13200	G=0.90811	C=0.00000, T=0.09189
Allele Frequency Aggregator	European	Sub	9330	G=0.8753	C=0.0000, T=0.1247
Allele Frequency Aggregator	African	Sub	2614	G=0.9985	C=0.0000, T=0.0015
Allele Frequency Aggregator	Other	Sub	528	G=0.913	C=0.000, T=0.087
Allele Frequency Aggregator	Latin American 2	Sub	450	G=1.000	C=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	C=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	98	G=1.00	C=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	68	G=1.00	C=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.8924	T=0.1076
1000Genomes_30x	African	Sub	1786	G=0.9770	T=0.0230
1000Genomes_30x	Europe	Sub	1266	G=0.7164	T=0.2836
1000Genomes_30x	South Asian	Sub	1202	G=0.8852	T=0.1148
1000Genomes_30x	East Asian	Sub	1170	G=0.9991	T=0.0009
1000Genomes_30x	American	Sub	980	G=0.847	T=0.153
1000Genomes	Global	Study-wide	5008	G=0.8944	T=0.1056
1000Genomes	African	Sub	1322	G=0.9766	T=0.0234
1000Genomes	East Asian	Sub	1008	G=0.9990	T=0.0010
1000Genomes	Europe	Sub	1006	G=0.7276	T=0.2724
1000Genomes	South Asian	Sub	978	G=0.889	T=0.111
1000Genomes	American	Sub	694	G=0.836	T=0.164
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7489	T=0.2511
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.6975	T=0.3025
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7176	T=0.2824
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.710	T=0.290
Northern Sweden	ACPOP	Study-wide	600	G=0.722	T=0.278
Qatari	Global	Study-wide	216	G=0.745	T=0.255
SGDP_PRJ	Global	Study-wide	106	G=0.434	T=0.566
Siberian	Global	Study-wide	10	G=0.5	T=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 2	NC_000002.12:g.29053144G>C
GRCh38.p14 chr 2	NC_000002.12:g.29053144G>T
GRCh37.p13 chr 2	NC_000002.11:g.29276010G>C
GRCh37.p13 chr 2	NC_000002.11:g.29276010G>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	G=	C	T
GRCh38.p14 chr 2	NC_000002.12:g.29053144=	NC_000002.12:g.29053144G>C	NC_000002.12:g.29053144G>T
GRCh37.p13 chr 2	NC_000002.11:g.29276010=	NC_000002.11:g.29276010G>C	NC_000002.11:g.29276010G>T
TOGARAM2 transcript variant 1	NM_199280.3:c.*1051=	NM_199280.3:c.*1051G>C	NM_199280.3:c.*1051G>T
TOGARAM2 transcript variant 2	NM_001321538.2:c.*1051=	NM_001321538.2:c.*1051G>C	NM_001321538.2:c.*1051G>T
TOGARAM2 transcript variant 3	NM_001321539.2:c.*1051=	NM_001321539.2:c.*1051G>C	NM_001321539.2:c.*1051G>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#.

47 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss21656509	Apr 05, 2004 (121)
2	ABI	ss41755373	Mar 14, 2006 (126)
3	HUMANGENOME_JCVI	ss96383961	Feb 03, 2009 (130)
4	1000GENOMES	ss109358874	Jan 24, 2009 (130)
5	ENSEMBL	ss135907272	Dec 01, 2009 (131)
6	COMPLETE_GENOMICS	ss164069395	Jul 04, 2010 (132)
7	1000GENOMES	ss219139275	Jul 14, 2010 (132)
8	1000GENOMES	ss231090163	Jul 14, 2010 (132)
9	PJP	ss292533961	May 09, 2011 (134)
10	SSMP	ss649019720	Apr 25, 2013 (138)
11	EVA-GONL	ss976625479	Aug 21, 2014 (142)
12	JMKIDD_LAB	ss1068960249	Aug 21, 2014 (142)
13	1000GENOMES	ss1296439595	Aug 21, 2014 (142)
14	DDI	ss1428517428	Apr 01, 2015 (144)
15	EVA_DECODE	ss1586031139	Apr 01, 2015 (144)
16	EVA_UK10K_ALSPAC	ss1603091315	Apr 01, 2015 (144)
17	EVA_UK10K_TWINSUK	ss1646085348	Apr 01, 2015 (144)
18	WEILL_CORNELL_DGM	ss1919857655	Feb 12, 2016 (147)
19	JJLAB	ss2020457312	Sep 14, 2016 (149)
20	USC_VALOUEV	ss2148502033	Dec 20, 2016 (150)
21	HUMAN_LONGEVITY	ss2228620923	Dec 20, 2016 (150)
22	GNOMAD	ss2771226401	Nov 08, 2017 (151)
23	SWEGEN	ss2989190304	Nov 08, 2017 (151)
24	BIOINF_KMB_FNS_UNIBA	ss3023995087	Nov 08, 2017 (151)
25	CSHL	ss3344135104	Nov 08, 2017 (151)
26	URBANLAB	ss3646993499	Oct 11, 2018 (152)
27	EGCUT_WGS	ss3657145372	Jul 13, 2019 (153)
28	EVA_DECODE	ss3703510912	Jul 13, 2019 (153)
29	ACPOP	ss3728265817	Jul 13, 2019 (153)
30	EVA	ss3756516855	Jul 13, 2019 (153)
31	KHV_HUMAN_GENOMES	ss3800896119	Jul 13, 2019 (153)
32	EVA	ss3826886099	Apr 25, 2020 (154)
33	SGDP_PRJ	ss3851864963	Apr 25, 2020 (154)
34	TOPMED	ss4498760756	Apr 26, 2021 (155)
35	TOPMED	ss4498760757	Apr 26, 2021 (155)
36	TOMMO_GENOMICS	ss5150469581	Apr 26, 2021 (155)
37	1000G_HIGH_COVERAGE	ss5247376582	Oct 17, 2022 (156)
38	EVA	ss5327664102	Oct 17, 2022 (156)
39	HUGCELL_USP	ss5447642806	Oct 17, 2022 (156)
40	EVA	ss5506336734	Oct 17, 2022 (156)
41	1000G_HIGH_COVERAGE	ss5522234612	Oct 17, 2022 (156)
42	SANFORD_IMAGENETICS	ss5628353636	Oct 17, 2022 (156)
43	TOMMO_GENOMICS	ss5678837038	Oct 17, 2022 (156)
44	EVA	ss5819833698	Oct 17, 2022 (156)
45	EVA	ss5929563659	Oct 17, 2022 (156)
46	EVA	ss5954557412	Oct 17, 2022 (156)
47	EVA	ss5980045534	Oct 17, 2022 (156)
48	1000Genomes	NC_000002.11 - 29276010	Oct 11, 2018 (152)
49	1000Genomes_30x	NC_000002.12 - 29053144	Oct 17, 2022 (156)
50	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 29276010	Oct 11, 2018 (152)
51	Genetic variation in the Estonian population	NC_000002.11 - 29276010	Oct 11, 2018 (152)
52	gnomAD - Genomes	NC_000002.12 - 29053144	Apr 26, 2021 (155)
53	Genome of the Netherlands Release 5	NC_000002.11 - 29276010	Apr 25, 2020 (154)
54	Northern Sweden	NC_000002.11 - 29276010	Jul 13, 2019 (153)
55	Qatari	NC_000002.11 - 29276010	Apr 25, 2020 (154)
56	SGDP_PRJ	NC_000002.11 - 29276010	Apr 25, 2020 (154)
57	Siberian	NC_000002.11 - 29276010	Apr 25, 2020 (154)
58	8.3KJPN	NC_000002.11 - 29276010	Apr 26, 2021 (155)
59	14KJPN	NC_000002.12 - 29053144	Oct 17, 2022 (156)
60	TopMed Submission ignored due to conflicting rows: Row 302583635 (NC_000002.12:29053143:G:C 2/264690) Row 302583636 (NC_000002.12:29053143:G:T 50462/264690)	-	Apr 26, 2021 (155)
61	TopMed Submission ignored due to conflicting rows: Row 302583635 (NC_000002.12:29053143:G:C 2/264690) Row 302583636 (NC_000002.12:29053143:G:T 50462/264690)	-	Apr 26, 2021 (155)
62	UK 10K study - Twins	NC_000002.11 - 29276010	Oct 11, 2018 (152)
63	ALFA	NC_000002.12 - 29053144	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
8640014125, ss4498760756	NC_000002.12:29053143:G:C	NC_000002.12:29053143:G:C	(self)
ss109358874, ss164069395, ss292533961, ss1586031139	NC_000002.10:29129513:G:T	NC_000002.12:29053143:G:T	(self)
7359565, 4085728, 2883620, 1794416, 1550682, 1899585, 3881943, 1018387, 8438888, 4085728, ss219139275, ss231090163, ss649019720, ss976625479, ss1068960249, ss1296439595, ss1428517428, ss1603091315, ss1646085348, ss1919857655, ss2020457312, ss2148502033, ss2771226401, ss2989190304, ss3344135104, ss3657145372, ss3728265817, ss3756516855, ss3826886099, ss3851864963, ss5150469581, ss5327664102, ss5506336734, ss5628353636, ss5819833698, ss5954557412, ss5980045534	NC_000002.11:29276009:G:T	NC_000002.12:29053143:G:T	(self)
9760547, 52300926, 12674142, 8640014125, ss2228620923, ss3023995087, ss3646993499, ss3703510912, ss3800896119, ss4498760757, ss5247376582, ss5447642806, ss5522234612, ss5678837038, ss5929563659	NC_000002.12:29053143:G:T	NC_000002.12:29053143:G:T	(self)
ss21656509	NT_022184.13:8091942:G:T	NC_000002.12:29053143:G:T	(self)
ss41755373, ss96383961, ss135907272	NT_022184.15:8097896:G:T	NC_000002.12:29053143:G: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 rs13011424

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

rs13011424