Name: rs13222726
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.

rs13222726

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:141928099 (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: A>G / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.229597 (60772/264690, TOPMED)
G=0.223702 (31295/139896, GnomAD)
G=0.26448 (8163/30864, ALFA) (+ 16 more)
G=0.40519 (11450/28258, 14KJPN)
G=0.40775 (6833/16758, 8.3KJPN)
G=0.2483 (1590/6404, 1000G_30x)
G=0.2534 (1269/5008, 1000G)
G=0.3125 (1400/4480, Estonian)
G=0.2701 (1041/3854, ALSPAC)
G=0.2759 (1023/3708, TWINSUK)
G=0.4133 (1211/2930, KOREAN)
G=0.4241 (777/1832, Korea1K)
G=0.271 (270/998, GoNL)
G=0.283 (170/600, NorthernSweden)
A=0.360 (103/286, SGDP_PRJ)
G=0.185 (40/216, Qatari)
G=0.386 (81/210, Vietnamese)
G=0.20 (8/40, GENOME_DK)
A=0.40 (12/30, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CLEC5A : Non Coding Transcript Variant
LOC124901761 : 2KB Upstream 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	30864	A=0.73552	G=0.26448
European	Sub	24736	A=0.71358	G=0.28642
African	Sub	3168	A=0.9366	G=0.0634
African Others	Sub	124	A=0.952	G=0.048
African American	Sub	3044	A=0.9359	G=0.0641
Asian	Sub	128	A=0.555	G=0.445
East Asian	Sub	100	A=0.60	G=0.40
Other Asian	Sub	28	A=0.39	G=0.61
Latin American 1	Sub	168	A=0.768	G=0.232
Latin American 2	Sub	700	A=0.637	G=0.363
South Asian	Sub	114	A=0.763	G=0.237
Other	Sub	1850	A=0.7297	G=0.2703

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	A=0.770403	G=0.229597
gnomAD - Genomes	Global	Study-wide	139896	A=0.776298	G=0.223702
gnomAD - Genomes	European	Sub	75766	A=0.72201	G=0.27799
gnomAD - Genomes	African	Sub	41938	A=0.92680	G=0.07320
gnomAD - Genomes	American	Sub	13604	A=0.68318	G=0.31682
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	A=0.7358	G=0.2642
gnomAD - Genomes	East Asian	Sub	3120	A=0.5295	G=0.4705
gnomAD - Genomes	Other	Sub	2148	A=0.7635	G=0.2365
Allele Frequency Aggregator	Total	Global	30864	A=0.73552	G=0.26448
Allele Frequency Aggregator	European	Sub	24736	A=0.71358	G=0.28642
Allele Frequency Aggregator	African	Sub	3168	A=0.9366	G=0.0634
Allele Frequency Aggregator	Other	Sub	1850	A=0.7297	G=0.2703
Allele Frequency Aggregator	Latin American 2	Sub	700	A=0.637	G=0.363
Allele Frequency Aggregator	Latin American 1	Sub	168	A=0.768	G=0.232
Allele Frequency Aggregator	Asian	Sub	128	A=0.555	G=0.445
Allele Frequency Aggregator	South Asian	Sub	114	A=0.763	G=0.237
14KJPN	JAPANESE	Study-wide	28258	A=0.59481	G=0.40519
8.3KJPN	JAPANESE	Study-wide	16758	A=0.59225	G=0.40775
1000Genomes_30x	Global	Study-wide	6404	A=0.7517	G=0.2483
1000Genomes_30x	African	Sub	1786	A=0.9636	G=0.0364
1000Genomes_30x	Europe	Sub	1266	A=0.7227	G=0.2773
1000Genomes_30x	South Asian	Sub	1202	A=0.7537	G=0.2463
1000Genomes_30x	East Asian	Sub	1170	A=0.5462	G=0.4538
1000Genomes_30x	American	Sub	980	A=0.646	G=0.354
1000Genomes	Global	Study-wide	5008	A=0.7466	G=0.2534
1000Genomes	African	Sub	1322	A=0.9629	G=0.0371
1000Genomes	East Asian	Sub	1008	A=0.5407	G=0.4593
1000Genomes	Europe	Sub	1006	A=0.7237	G=0.2763
1000Genomes	South Asian	Sub	978	A=0.760	G=0.240
1000Genomes	American	Sub	694	A=0.648	G=0.352
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.6875	G=0.3125
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.7299	G=0.2701
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.7241	G=0.2759
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.5867	G=0.4133, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	A=0.5759	G=0.4241
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.729	G=0.271
Northern Sweden	ACPOP	Study-wide	600	A=0.717	G=0.283
SGDP_PRJ	Global	Study-wide	286	A=0.360	G=0.640
Qatari	Global	Study-wide	216	A=0.815	G=0.185
A Vietnamese Genetic Variation Database	Global	Study-wide	210	A=0.614	G=0.386
The Danish reference pan genome	Danish	Study-wide	40	A=0.80	G=0.20
Siberian	Global	Study-wide	30	A=0.40	G=0.60

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 7	NC_000007.14:g.141928099A>G
GRCh38.p14 chr 7	NC_000007.14:g.141928099A>T
GRCh37.p13 chr 7	NC_000007.13:g.141627899A>G
GRCh37.p13 chr 7	NC_000007.13:g.141627899A>T
GRCh37.p13 chr 7 fix patch HG7_PATCH	NW_003571040.1:g.70050A>G
GRCh37.p13 chr 7 fix patch HG7_PATCH	NW_003571040.1:g.70050A>T

Gene: CLEC5A, C-type lectin domain containing 5A (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CLEC5A transcript variant 1	NM_013252.3:c.*2005=	N/A	3 Prime UTR Variant
CLEC5A transcript variant 2	NM_001301167.2:c.*2005=	N/A	3 Prime UTR Variant
CLEC5A transcript variant X2	XM_011515995.3:c.*2005=	N/A	3 Prime UTR Variant
CLEC5A transcript variant X1	XR_007059995.1:n.1943T>C	N/A	Non Coding Transcript Variant
CLEC5A transcript variant X1	XR_007059995.1:n.1943T>A	N/A	Non Coding Transcript Variant

Gene: LOC124901761, uncharacterized LOC124901761 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124901761 transcript	XR_007060564.1:n.	N/A	Upstream 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	A=	G	T
GRCh38.p14 chr 7	NC_000007.14:g.141928099=	NC_000007.14:g.141928099A>G	NC_000007.14:g.141928099A>T
GRCh37.p13 chr 7	NC_000007.13:g.141627899=	NC_000007.13:g.141627899A>G	NC_000007.13:g.141627899A>T
GRCh37.p13 chr 7 fix patch HG7_PATCH	NW_003571040.1:g.70050=	NW_003571040.1:g.70050A>G	NW_003571040.1:g.70050A>T
CLEC5A transcript variant 1	NM_013252.3:c.*2005=	NM_013252.3:c.*2005T>C	NM_013252.3:c.*2005T>A
CLEC5A transcript variant 1	NM_013252.2:c.*2005=	NM_013252.2:c.*2005T>C	NM_013252.2:c.*2005T>A
CLEC5A transcript variant X2	XM_011515995.3:c.*2005=	XM_011515995.3:c.*2005T>C	XM_011515995.3:c.*2005T>A
CLEC5A transcript variant X3	XM_011515995.2:c.*2005=	XM_011515995.2:c.*2005T>C	XM_011515995.2:c.*2005T>A
CLEC5A transcript variant X2	XM_011515995.1:c.*2005=	XM_011515995.1:c.*2005T>C	XM_011515995.1:c.*2005T>A
CLEC5A transcript variant 2	NM_001301167.2:c.*2005=	NM_001301167.2:c.*2005T>C	NM_001301167.2:c.*2005T>A
CLEC5A transcript variant 2	NM_001301167.1:c.*2005=	NM_001301167.1:c.*2005T>C	NM_001301167.1:c.*2005T>A
CLEC5A transcript variant X1	XR_007059995.1:n.1943=	XR_007059995.1:n.1943T>C	XR_007059995.1:n.1943T>A

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#.

78 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss22526324	Apr 05, 2004 (121)
2	PERLEGEN	ss24032168	Sep 20, 2004 (123)
3	ABI	ss42919655	Mar 15, 2006 (126)
4	HGSV	ss84177798	Dec 15, 2007 (130)
5	BCMHGSC_JDW	ss93779239	Mar 25, 2008 (129)
6	BGI	ss105578859	Feb 06, 2009 (130)
7	1000GENOMES	ss114548522	Jan 25, 2009 (130)
8	ENSEMBL	ss133798651	Dec 01, 2009 (131)
9	ENSEMBL	ss143028113	Dec 01, 2009 (131)
10	GMI	ss155604144	Dec 01, 2009 (131)
11	COMPLETE_GENOMICS	ss162791150	Jul 04, 2010 (132)
12	COMPLETE_GENOMICS	ss165557920	Jul 04, 2010 (132)
13	BCM-HGSC-SUB	ss208300811	Jul 04, 2010 (132)
14	1000GENOMES	ss210695365	Jul 14, 2010 (132)
15	1000GENOMES	ss234199583	Jul 15, 2010 (132)
16	1000GENOMES	ss241105862	Jul 15, 2010 (132)
17	GMI	ss279562640	May 04, 2012 (137)
18	GMI	ss285733799	Apr 25, 2013 (138)
19	PJP	ss293981167	May 09, 2011 (134)
20	ILLUMINA	ss483493775	May 04, 2012 (137)
21	ILLUMINA	ss485364625	May 04, 2012 (137)
22	ILLUMINA	ss535702236	Sep 11, 2015 (146)
23	TISHKOFF	ss560356071	Apr 25, 2013 (138)
24	SSMP	ss654769073	Apr 25, 2013 (138)
25	ILLUMINA	ss779508644	Sep 11, 2015 (146)
26	ILLUMINA	ss782190292	Sep 11, 2015 (146)
27	ILLUMINA	ss834978970	Sep 11, 2015 (146)
28	EVA-GONL	ss984891079	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1075049054	Aug 21, 2014 (142)
30	1000GENOMES	ss1327486182	Aug 21, 2014 (142)
31	DDI	ss1431305104	Apr 09, 2015 (144)
32	EVA_GENOME_DK	ss1582436373	Apr 09, 2015 (144)
33	EVA_DECODE	ss1594480968	Apr 01, 2015 (144)
34	EVA_UK10K_ALSPAC	ss1619404778	Apr 09, 2015 (144)
35	EVA_UK10K_TWINSUK	ss1662398811	Apr 09, 2015 (144)
36	WEILL_CORNELL_DGM	ss1928146205	Feb 17, 2016 (147)
37	GENOMED	ss1970835758	Sep 28, 2016 (149)
38	JJLAB	ss2024762594	Sep 28, 2016 (149)
39	USC_VALOUEV	ss2152985472	Oct 12, 2018 (152)
40	HUMAN_LONGEVITY	ss2298589150	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2626868580	Oct 12, 2018 (152)
42	ILLUMINA	ss2634671019	Oct 12, 2018 (152)
43	GRF	ss2708708072	Oct 12, 2018 (152)
44	GNOMAD	ss2860112963	Oct 12, 2018 (152)
45	SWEGEN	ss3002177817	Oct 12, 2018 (152)
46	BIOINF_KMB_FNS_UNIBA	ss3026170383	Nov 08, 2017 (151)
47	CSHL	ss3347883612	Oct 12, 2018 (152)
48	ILLUMINA	ss3629933201	Oct 12, 2018 (152)
49	ILLUMINA	ss3632574698	Oct 12, 2018 (152)
50	URBANLAB	ss3648771132	Oct 12, 2018 (152)
51	EGCUT_WGS	ss3669937071	Jul 13, 2019 (153)
52	EVA_DECODE	ss3720866663	Jul 13, 2019 (153)
53	ACPOP	ss3735147818	Jul 13, 2019 (153)
54	EVA	ss3767268052	Jul 13, 2019 (153)
55	KHV_HUMAN_GENOMES	ss3810434323	Jul 13, 2019 (153)
56	EVA	ss3825730561	Apr 26, 2020 (154)
57	EVA	ss3830864761	Apr 26, 2020 (154)
58	SGDP_PRJ	ss3868578814	Apr 26, 2020 (154)
59	KRGDB	ss3915955094	Apr 26, 2020 (154)
60	KOGIC	ss3962760499	Apr 26, 2020 (154)
61	FSA-LAB	ss3984382977	Apr 26, 2021 (155)
62	EVA	ss3986041744	Apr 26, 2021 (155)
63	GNOMAD	ss4174659525	Apr 26, 2021 (155)
64	TOPMED	ss4766837468	Apr 26, 2021 (155)
65	TOMMO_GENOMICS	ss5185988019	Apr 26, 2021 (155)
66	1000G_HIGH_COVERAGE	ss5275050573	Oct 14, 2022 (156)
67	EVA	ss5315285261	Oct 14, 2022 (156)
68	EVA	ss5377347582	Oct 14, 2022 (156)
69	HUGCELL_USP	ss5471903825	Oct 14, 2022 (156)
70	EVA	ss5509163274	Oct 14, 2022 (156)
71	1000G_HIGH_COVERAGE	ss5564361866	Oct 14, 2022 (156)
72	SANFORD_IMAGENETICS	ss5644162251	Oct 14, 2022 (156)
73	TOMMO_GENOMICS	ss5727105699	Oct 14, 2022 (156)
74	YY_MCH	ss5809168262	Oct 14, 2022 (156)
75	EVA	ss5823645955	Oct 14, 2022 (156)
76	EVA	ss5856132050	Oct 14, 2022 (156)
77	EVA	ss5861242434	Oct 14, 2022 (156)
78	EVA	ss5973368075	Oct 14, 2022 (156)
79	1000Genomes	NC_000007.13 - 141627899	Oct 12, 2018 (152)
80	1000Genomes_30x	NC_000007.14 - 141928099	Oct 14, 2022 (156)
81	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 141627899	Oct 12, 2018 (152)
82	Genetic variation in the Estonian population	NC_000007.13 - 141627899	Oct 12, 2018 (152)
83	The Danish reference pan genome	NC_000007.13 - 141627899	Apr 26, 2020 (154)
84	gnomAD - Genomes	NC_000007.14 - 141928099	Apr 26, 2021 (155)
85	Genome of the Netherlands Release 5	NC_000007.13 - 141627899	Apr 26, 2020 (154)
86	KOREAN population from KRGDB	NC_000007.13 - 141627899	Apr 26, 2020 (154)
87	Korean Genome Project	NC_000007.14 - 141928099	Apr 26, 2020 (154)
88	Northern Sweden	NC_000007.13 - 141627899	Jul 13, 2019 (153)
89	Qatari	NC_000007.13 - 141627899	Apr 26, 2020 (154)
90	SGDP_PRJ	NC_000007.13 - 141627899	Apr 26, 2020 (154)
91	Siberian	NC_000007.13 - 141627899	Apr 26, 2020 (154)
92	8.3KJPN	NC_000007.13 - 141627899	Apr 26, 2021 (155)
93	14KJPN	NC_000007.14 - 141928099	Oct 14, 2022 (156)
94	TopMed	NC_000007.14 - 141928099	Apr 26, 2021 (155)
95	UK 10K study - Twins	NC_000007.13 - 141627899	Oct 12, 2018 (152)
96	A Vietnamese Genetic Variation Database	NC_000007.13 - 141627899	Jul 13, 2019 (153)
97	ALFA	NC_000007.14 - 141928099	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)
rs60105876	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss84177798	NC_000007.11:141081082:A:G	NC_000007.14:141928098:A:G	(self)
ss93779239, ss114548522, ss162791150, ss165557920, ss208300811, ss210695365, ss279562640, ss285733799, ss293981167, ss485364625, ss1594480968	NC_000007.12:141274367:A:G	NC_000007.14:141928098:A:G	(self)
39543292, 22009487, 15675319, 8601311, 9819138, 23132488, 8432683, 10188135, 20595794, 5501826, 43957326, 22009487, 4900071, ss234199583, ss241105862, ss483493775, ss535702236, ss560356071, ss654769073, ss779508644, ss782190292, ss834978970, ss984891079, ss1075049054, ss1327486182, ss1431305104, ss1582436373, ss1619404778, ss1662398811, ss1928146205, ss1970835758, ss2024762594, ss2152985472, ss2626868580, ss2634671019, ss2708708072, ss2860112963, ss3002177817, ss3347883612, ss3629933201, ss3632574698, ss3669937071, ss3735147818, ss3767268052, ss3825730561, ss3830864761, ss3868578814, ss3915955094, ss3984382977, ss3986041744, ss5185988019, ss5315285261, ss5377347582, ss5509163274, ss5644162251, ss5823645955, ss5973368075	NC_000007.13:141627898:A:G	NC_000007.14:141928098:A:G	(self)
51887801, 279237166, 19138500, 60942803, 604215027, 6723993316, ss2298589150, ss3026170383, ss3648771132, ss3720866663, ss3810434323, ss3962760499, ss4174659525, ss4766837468, ss5275050573, ss5471903825, ss5564361866, ss5727105699, ss5809168262, ss5856132050, ss5861242434	NC_000007.14:141928098:A:G	NC_000007.14:141928098:A:G	(self)
ss22526324	NT_007914.13:2219450:A:G	NC_000007.14:141928098:A:G	(self)
ss24032168, ss42919655, ss105578859, ss133798651, ss143028113, ss155604144	NT_007914.15:2223521:A:G	NC_000007.14:141928098:A:G	(self)
23132488, ss3915955094	NC_000007.13:141627898:A:T	NC_000007.14:141928098:A: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 rs13222726

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

rs13222726