Name: rs11703021
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.

rs11703021

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:46382600 (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: T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.169119 (44764/264690, TOPMED)
C=0.167983 (23522/140026, GnomAD)
C=0.01745 (493/28258, 14KJPN) (+ 16 more)
C=0.13621 (2573/18890, ALFA)
C=0.01695 (284/16760, 8.3KJPN)
C=0.1565 (1002/6404, 1000G_30x)
C=0.1514 (758/5008, 1000G)
C=0.1018 (456/4480, Estonian)
C=0.0947 (365/3854, ALSPAC)
C=0.0885 (328/3708, TWINSUK)
C=0.0116 (34/2922, KOREAN)
C=0.0169 (31/1832, Korea1K)
C=0.100 (100/998, GoNL)
C=0.058 (35/600, NorthernSweden)
C=0.111 (24/216, Qatari)
C=0.009 (2/214, Vietnamese)
T=0.41 (38/92, SGDP_PRJ)
T=0.5 (1/2, Siberian)
C=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CELSR1 : 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18890	T=0.86379	C=0.13621
European	Sub	14286	T=0.90487	C=0.09513
African	Sub	2946	T=0.6497	C=0.3503
African Others	Sub	114	T=0.640	C=0.360
African American	Sub	2832	T=0.6501	C=0.3499
Asian	Sub	112	T=0.955	C=0.045
East Asian	Sub	86	T=0.98	C=0.02
Other Asian	Sub	26	T=0.88	C=0.12
Latin American 1	Sub	146	T=0.877	C=0.123
Latin American 2	Sub	610	T=0.930	C=0.070
South Asian	Sub	98	T=0.91	C=0.09
Other	Sub	692	T=0.845	C=0.155

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	T=0.830881	C=0.169119
gnomAD - Genomes	Global	Study-wide	140026	T=0.832017	C=0.167983
gnomAD - Genomes	European	Sub	75884	T=0.90957	C=0.09043
gnomAD - Genomes	African	Sub	41900	T=0.64955	C=0.35045
gnomAD - Genomes	American	Sub	13640	T=0.91114	C=0.08886
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.8782	C=0.1218
gnomAD - Genomes	East Asian	Sub	3128	T=0.9821	C=0.0179
gnomAD - Genomes	Other	Sub	2150	T=0.8591	C=0.1409
14KJPN	JAPANESE	Study-wide	28258	T=0.98255	C=0.01745
Allele Frequency Aggregator	Total	Global	18890	T=0.86379	C=0.13621
Allele Frequency Aggregator	European	Sub	14286	T=0.90487	C=0.09513
Allele Frequency Aggregator	African	Sub	2946	T=0.6497	C=0.3503
Allele Frequency Aggregator	Other	Sub	692	T=0.845	C=0.155
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.930	C=0.070
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.877	C=0.123
Allele Frequency Aggregator	Asian	Sub	112	T=0.955	C=0.045
Allele Frequency Aggregator	South Asian	Sub	98	T=0.91	C=0.09
8.3KJPN	JAPANESE	Study-wide	16760	T=0.98305	C=0.01695
1000Genomes_30x	Global	Study-wide	6404	T=0.8435	C=0.1565
1000Genomes_30x	African	Sub	1786	T=0.5901	C=0.4099
1000Genomes_30x	Europe	Sub	1266	T=0.9060	C=0.0940
1000Genomes_30x	South Asian	Sub	1202	T=0.9567	C=0.0433
1000Genomes_30x	East Asian	Sub	1170	T=0.9863	C=0.0137
1000Genomes_30x	American	Sub	980	T=0.915	C=0.085
1000Genomes	Global	Study-wide	5008	T=0.8486	C=0.1514
1000Genomes	African	Sub	1322	T=0.5893	C=0.4107
1000Genomes	East Asian	Sub	1008	T=0.9871	C=0.0129
1000Genomes	Europe	Sub	1006	T=0.9046	C=0.0954
1000Genomes	South Asian	Sub	978	T=0.953	C=0.047
1000Genomes	American	Sub	694	T=0.914	C=0.086
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.8982	C=0.1018
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9053	C=0.0947
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9115	C=0.0885
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9884	C=0.0116
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9831	C=0.0169
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.900	C=0.100
Northern Sweden	ACPOP	Study-wide	600	T=0.942	C=0.058
Qatari	Global	Study-wide	216	T=0.889	C=0.111
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.991	C=0.009
SGDP_PRJ	Global	Study-wide	92	T=0.41	C=0.59
Siberian	Global	Study-wide	2	T=0.5	C=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 22	NC_000022.11:g.46382600T>C
GRCh37.p13 chr 22	NC_000022.10:g.46778497T>C
CELSR1 RefSeqGene	NG_030466.2:g.159571A>G

Gene: CELSR1, cadherin EGF LAG seven-pass G-type receptor 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CELSR1 transcript variant 1	NM_001378328.1:c.6884-550… NM_001378328.1:c.6884-550A>G	N/A	Intron Variant
CELSR1 transcript variant 2	NM_014246.4:c.6884-550A>G	N/A	Intron Variant
CELSR1 transcript variant X3	XM_011530554.3:c.3377-550… XM_011530554.3:c.3377-550A>G	N/A	Intron Variant
CELSR1 transcript variant X4	XM_011530555.3:c.3281-550… XM_011530555.3:c.3281-550A>G	N/A	Intron Variant
CELSR1 transcript variant X1	XM_047441624.1:c.6884-550… XM_047441624.1:c.6884-550A>G	N/A	Intron Variant
CELSR1 transcript variant X2	XM_011530553.2:c.	N/A	Genic Downstream 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	T=	C
GRCh38.p14 chr 22	NC_000022.11:g.46382600=	NC_000022.11:g.46382600T>C
GRCh37.p13 chr 22	NC_000022.10:g.46778497=	NC_000022.10:g.46778497T>C
CELSR1 RefSeqGene	NG_030466.2:g.159571=	NG_030466.2:g.159571A>G
CELSR1 transcript variant 1	NM_001378328.1:c.6884-550=	NM_001378328.1:c.6884-550A>G
CELSR1 transcript	NM_014246.1:c.6884-550=	NM_014246.1:c.6884-550A>G
CELSR1 transcript variant 2	NM_014246.4:c.6884-550=	NM_014246.4:c.6884-550A>G
CELSR1 transcript variant X3	XM_011530554.3:c.3377-550=	XM_011530554.3:c.3377-550A>G
CELSR1 transcript variant X4	XM_011530555.3:c.3281-550=	XM_011530555.3:c.3281-550A>G
CELSR1 transcript variant X1	XM_047441624.1:c.6884-550=	XM_047441624.1:c.6884-550A>G

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#.

50 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss16918691	Feb 28, 2004 (120)
2	HGSV	ss82050205	Dec 15, 2007 (130)
3	1000GENOMES	ss114309289	Jan 25, 2009 (130)
4	COMPLETE_GENOMICS	ss169476556	Jul 04, 2010 (132)
5	BUSHMAN	ss204111918	Jul 04, 2010 (132)
6	1000GENOMES	ss228718694	Jul 14, 2010 (132)
7	1000GENOMES	ss238096279	Jul 15, 2010 (132)
8	TISHKOFF	ss566692602	Apr 25, 2013 (138)
9	SSMP	ss662621170	Apr 25, 2013 (138)
10	EVA-GONL	ss995431643	Aug 21, 2014 (142)
11	JMKIDD_LAB	ss1082714344	Aug 21, 2014 (142)
12	1000GENOMES	ss1367478444	Aug 21, 2014 (142)
13	DDI	ss1429280190	Apr 01, 2015 (144)
14	EVA_UK10K_ALSPAC	ss1640157819	Apr 01, 2015 (144)
15	EVA_UK10K_TWINSUK	ss1683151852	Apr 01, 2015 (144)
16	EVA_DECODE	ss1699503064	Apr 01, 2015 (144)
17	HAMMER_LAB	ss1809823977	Sep 08, 2015 (146)
18	WEILL_CORNELL_DGM	ss1939002705	Feb 12, 2016 (147)
19	JJLAB	ss2030273584	Sep 14, 2016 (149)
20	USC_VALOUEV	ss2158896645	Dec 20, 2016 (150)
21	HUMAN_LONGEVITY	ss2247970144	Dec 20, 2016 (150)
22	GRF	ss2704649150	Nov 08, 2017 (151)
23	GNOMAD	ss2975292578	Nov 08, 2017 (151)
24	SWEGEN	ss3019434950	Nov 08, 2017 (151)
25	BIOINF_KMB_FNS_UNIBA	ss3028973353	Nov 08, 2017 (151)
26	CSHL	ss3352873958	Nov 08, 2017 (151)
27	EGCUT_WGS	ss3685924605	Jul 13, 2019 (153)
28	EVA_DECODE	ss3708360072	Jul 13, 2019 (153)
29	ACPOP	ss3744001589	Jul 13, 2019 (153)
30	EVA	ss3759479723	Jul 13, 2019 (153)
31	PACBIO	ss3788847810	Jul 13, 2019 (153)
32	PACBIO	ss3793709900	Jul 13, 2019 (153)
33	PACBIO	ss3798596427	Jul 13, 2019 (153)
34	KHV_HUMAN_GENOMES	ss3822637777	Jul 13, 2019 (153)
35	EVA	ss3836031477	Apr 27, 2020 (154)
36	SGDP_PRJ	ss3890718034	Apr 27, 2020 (154)
37	KRGDB	ss3941123702	Apr 27, 2020 (154)
38	KOGIC	ss3983811019	Apr 27, 2020 (154)
39	TOPMED	ss5111974777	Apr 27, 2021 (155)
40	TOMMO_GENOMICS	ss5233005942	Apr 27, 2021 (155)
41	1000G_HIGH_COVERAGE	ss5311383516	Oct 16, 2022 (156)
42	EVA	ss5441820035	Oct 16, 2022 (156)
43	HUGCELL_USP	ss5503198251	Oct 16, 2022 (156)
44	1000G_HIGH_COVERAGE	ss5619068171	Oct 16, 2022 (156)
45	SANFORD_IMAGENETICS	ss5664648995	Oct 16, 2022 (156)
46	TOMMO_GENOMICS	ss5794251573	Oct 16, 2022 (156)
47	YY_MCH	ss5818778907	Oct 16, 2022 (156)
48	EVA	ss5822182425	Oct 16, 2022 (156)
49	EVA	ss5882137221	Oct 16, 2022 (156)
50	EVA	ss5959507588	Oct 16, 2022 (156)
51	1000Genomes	NC_000022.10 - 46778497	Oct 12, 2018 (152)
52	1000Genomes_30x	NC_000022.11 - 46382600	Oct 16, 2022 (156)
53	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 46778497	Oct 12, 2018 (152)
54	Genetic variation in the Estonian population	NC_000022.10 - 46778497	Oct 12, 2018 (152)
55	gnomAD - Genomes	NC_000022.11 - 46382600	Apr 27, 2021 (155)
56	Genome of the Netherlands Release 5	NC_000022.10 - 46778497	Apr 27, 2020 (154)
57	KOREAN population from KRGDB	NC_000022.10 - 46778497	Apr 27, 2020 (154)
58	Korean Genome Project	NC_000022.11 - 46382600	Apr 27, 2020 (154)
59	Northern Sweden	NC_000022.10 - 46778497	Jul 13, 2019 (153)
60	Qatari	NC_000022.10 - 46778497	Apr 27, 2020 (154)
61	SGDP_PRJ	NC_000022.10 - 46778497	Apr 27, 2020 (154)
62	Siberian	NC_000022.10 - 46778497	Apr 27, 2020 (154)
63	8.3KJPN	NC_000022.10 - 46778497	Apr 27, 2021 (155)
64	14KJPN	NC_000022.11 - 46382600	Oct 16, 2022 (156)
65	TopMed	NC_000022.11 - 46382600	Apr 27, 2021 (155)
66	UK 10K study - Twins	NC_000022.10 - 46778497	Oct 12, 2018 (152)
67	A Vietnamese Genetic Variation Database	NC_000022.10 - 46778497	Jul 13, 2019 (153)
68	ALFA	NC_000022.11 - 46382600	Apr 27, 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)
rs60450089	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss82050205	NC_000022.8:45099015:T:C	NC_000022.11:46382599:T:C	(self)
ss114309289, ss169476556, ss204111918, ss1699503064	NC_000022.9:45157160:T:C	NC_000022.11:46382599:T:C	(self)
81041867, 44829032, 31662853, 19971607, 48301096, 17286454, 21044627, 42735014, 11412999, 90975249, 44829032, 9884763, ss228718694, ss238096279, ss566692602, ss662621170, ss995431643, ss1082714344, ss1367478444, ss1429280190, ss1640157819, ss1683151852, ss1809823977, ss1939002705, ss2030273584, ss2158896645, ss2704649150, ss2975292578, ss3019434950, ss3352873958, ss3685924605, ss3744001589, ss3759479723, ss3788847810, ss3793709900, ss3798596427, ss3836031477, ss3890718034, ss3941123702, ss5233005942, ss5441820035, ss5664648995, ss5822182425, ss5959507588	NC_000022.10:46778496:T:C	NC_000022.11:46382599:T:C	(self)
106594106, 572268454, 40189020, 128088677, 387083724, 7378958070, ss2247970144, ss3028973353, ss3708360072, ss3822637777, ss3983811019, ss5111974777, ss5311383516, ss5503198251, ss5619068171, ss5794251573, ss5818778907, ss5882137221	NC_000022.11:46382599:T:C	NC_000022.11:46382599:T:C	(self)
ss16918691	NT_011523.9:358380:T:C	NC_000022.11:46382599:T:C	(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 rs11703021

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

rs11703021