Name: rs7466134
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.

rs7466134

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr9:20177211 (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>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.022132 (5858/264690, TOPMED)
C=0.020283 (2842/140116, GnomAD)
C=0.00000 (0/28258, 14KJPN) (+ 15 more)
C=0.01043 (197/18890, ALFA)
C=0.00000 (0/16760, 8.3KJPN)
C=0.0181 (116/6404, 1000G_30x)
C=0.0160 (80/5008, 1000G)
C=0.0008 (3/3854, ALSPAC)
C=0.0005 (2/3708, TWINSUK)
C=0.0000 (0/2930, KOREAN)
A=0.0000 (0/2930, KOREAN)
C=0.0000 (0/1832, Korea1K)
C=0.001 (1/998, GoNL)
C=0.000 (0/600, NorthernSweden)
C=0.005 (3/558, SGDP_PRJ)
C=0.000 (0/216, Qatari)
C=0.00 (0/54, Siberian)
C=0.00 (0/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SLC24A2 : 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	C=0.01043	T=0.98957
European	Sub	14286	C=0.00049	T=0.99951
African	Sub	2946	C=0.0580	T=0.9420
African Others	Sub	114	C=0.053	T=0.947
African American	Sub	2832	C=0.0583	T=0.9417
Asian	Sub	112	C=0.000	T=1.000
East Asian	Sub	86	C=0.00	T=1.00
Other Asian	Sub	26	C=0.00	T=1.00
Latin American 1	Sub	146	C=0.014	T=0.986
Latin American 2	Sub	610	C=0.005	T=0.995
South Asian	Sub	98	C=0.00	T=1.00
Other	Sub	692	C=0.020	T=0.980

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=0.022132	T=0.977868
gnomAD - Genomes	Global	Study-wide	140116	C=0.020283	T=0.979717
gnomAD - Genomes	European	Sub	75912	C=0.00095	T=0.99905
gnomAD - Genomes	African	Sub	42006	C=0.06006	T=0.93994
gnomAD - Genomes	American	Sub	13618	C=0.01366	T=0.98634
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.0057	T=0.9943
gnomAD - Genomes	East Asian	Sub	3108	C=0.0000	T=1.0000
gnomAD - Genomes	Other	Sub	2150	C=0.0195	T=0.9805
14KJPN	JAPANESE	Study-wide	28258	C=0.00000	T=1.00000
Allele Frequency Aggregator	Total	Global	18890	C=0.01043	T=0.98957
Allele Frequency Aggregator	European	Sub	14286	C=0.00049	T=0.99951
Allele Frequency Aggregator	African	Sub	2946	C=0.0580	T=0.9420
Allele Frequency Aggregator	Other	Sub	692	C=0.020	T=0.980
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.005	T=0.995
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.014	T=0.986
Allele Frequency Aggregator	Asian	Sub	112	C=0.000	T=1.000
Allele Frequency Aggregator	South Asian	Sub	98	C=0.00	T=1.00
8.3KJPN	JAPANESE	Study-wide	16760	C=0.00000	T=1.00000
1000Genomes_30x	Global	Study-wide	6404	C=0.0181	T=0.9819
1000Genomes_30x	African	Sub	1786	C=0.0560	T=0.9440
1000Genomes_30x	Europe	Sub	1266	C=0.0039	T=0.9961
1000Genomes_30x	South Asian	Sub	1202	C=0.0000	T=1.0000
1000Genomes_30x	East Asian	Sub	1170	C=0.0000	T=1.0000
1000Genomes_30x	American	Sub	980	C=0.011	T=0.989
1000Genomes	Global	Study-wide	5008	C=0.0160	T=0.9840
1000Genomes	African	Sub	1322	C=0.0530	T=0.9470
1000Genomes	East Asian	Sub	1008	C=0.0000	T=1.0000
1000Genomes	Europe	Sub	1006	C=0.0030	T=0.9970
1000Genomes	South Asian	Sub	978	C=0.000	T=1.000
1000Genomes	American	Sub	694	C=0.010	T=0.990
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.0008	T=0.9992
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.0005	T=0.9995
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.0000	A=0.0000, T=1.0000
Korean Genome Project	KOREAN	Study-wide	1832	C=0.0000	T=1.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.001	T=0.999
Northern Sweden	ACPOP	Study-wide	600	C=0.000	T=1.000
SGDP_PRJ	Global	Study-wide	558	C=0.005	T=0.995
Qatari	Global	Study-wide	216	C=0.000	T=1.000
Siberian	Global	Study-wide	54	C=0.00	T=1.00
The Danish reference pan genome	Danish	Study-wide	40	C=0.00	T=1.00

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 9	NC_000009.12:g.20177211C>A
GRCh38.p14 chr 9	NC_000009.12:g.20177211C>T
GRCh37.p13 chr 9	NC_000009.11:g.20177209C>A
GRCh37.p13 chr 9	NC_000009.11:g.20177209C>T

Gene: SLC24A2, solute carrier family 24 member 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC24A2 transcript variant 2	NM_001193288.3:c.	N/A	Genic Upstream Transcript Variant
SLC24A2 transcript variant 3	NM_001375850.1:c.	N/A	Genic Upstream Transcript Variant
SLC24A2 transcript variant 4	NM_001375851.1:c.	N/A	Genic Upstream Transcript Variant
SLC24A2 transcript variant 1	NM_020344.4:c.	N/A	Genic Upstream Transcript Variant
SLC24A2 transcript variant X1	XM_017014592.2:c.-529+124… XM_017014592.2:c.-529+124015G>T	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=	A	T
GRCh38.p14 chr 9	NC_000009.12:g.20177211=	NC_000009.12:g.20177211C>A	NC_000009.12:g.20177211C>T
GRCh37.p13 chr 9	NC_000009.11:g.20177209=	NC_000009.11:g.20177209C>A	NC_000009.11:g.20177209C>T
SLC24A2 transcript variant X1	XM_017014592.2:c.-529+124015=	XM_017014592.2:c.-529+124015G>T	XM_017014592.2:c.-529+124015G>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#.

72 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss11274917	Jul 11, 2003 (116)
2	SC_SNP	ss15539534	Feb 27, 2004 (120)
3	CSHL-HAPMAP	ss19796669	Feb 27, 2004 (120)
4	SSAHASNP	ss22782923	Apr 05, 2004 (121)
5	ABI	ss43433570	Mar 14, 2006 (126)
6	HGSV	ss77822423	Dec 07, 2007 (129)
7	HGSV	ss86198915	Dec 15, 2007 (130)
8	BCMHGSC_JDW	ss94026395	Mar 25, 2008 (129)
9	HUMANGENOME_JCVI	ss97713066	Feb 05, 2009 (130)
10	BGI	ss105668388	Feb 05, 2009 (130)
11	1000GENOMES	ss108662018	Jan 23, 2009 (130)
12	1000GENOMES	ss114278146	Jan 25, 2009 (130)
13	ILLUMINA-UK	ss115705733	Feb 14, 2009 (130)
14	ENSEMBL	ss134186037	Dec 01, 2009 (131)
15	ENSEMBL	ss144004743	Dec 01, 2009 (131)
16	GMI	ss157284925	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss164732724	Jul 04, 2010 (132)
18	BUSHMAN	ss200202452	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss206698671	Jul 04, 2010 (132)
20	1000GENOMES	ss224168305	Jul 14, 2010 (132)
21	1000GENOMES	ss234759323	Jul 15, 2010 (132)
22	1000GENOMES	ss241545547	Jul 15, 2010 (132)
23	GMI	ss280143283	May 04, 2012 (137)
24	GMI	ss285985771	Apr 25, 2013 (138)
25	PJP	ss294413864	May 09, 2011 (134)
26	SSMP	ss655724760	Apr 25, 2013 (138)
27	EVA-GONL	ss986398302	Aug 21, 2014 (142)
28	JMKIDD_LAB	ss1076181529	Aug 21, 2014 (142)
29	1000GENOMES	ss1333235363	Aug 21, 2014 (142)
30	DDI	ss1431778213	Apr 01, 2015 (144)
31	EVA_GENOME_DK	ss1583023336	Apr 01, 2015 (144)
32	EVA_UK10K_ALSPAC	ss1622423964	Apr 01, 2015 (144)
33	EVA_UK10K_TWINSUK	ss1665417997	Apr 01, 2015 (144)
34	HAMMER_LAB	ss1805917375	Sep 08, 2015 (146)
35	WEILL_CORNELL_DGM	ss1929682015	Feb 12, 2016 (147)
36	GENOMED	ss1971175208	Jul 19, 2016 (147)
37	JJLAB	ss2025553190	Sep 14, 2016 (149)
38	USC_VALOUEV	ss2153779368	Dec 20, 2016 (150)
39	HUMAN_LONGEVITY	ss2310083819	Dec 20, 2016 (150)
40	SYSTEMSBIOZJU	ss2627250682	Nov 08, 2017 (151)
41	GRF	ss2709582427	Nov 08, 2017 (151)
42	GNOMAD	ss2876357219	Nov 08, 2017 (151)
43	SWEGEN	ss3004512968	Nov 08, 2017 (151)
44	BIOINF_KMB_FNS_UNIBA	ss3026566550	Nov 08, 2017 (151)
45	CSHL	ss3348563478	Nov 08, 2017 (151)
46	URBANLAB	ss3649090332	Oct 12, 2018 (152)
47	EVA_DECODE	ss3723633074	Jul 13, 2019 (153)
48	ACPOP	ss3736381093	Jul 13, 2019 (153)
49	EVA	ss3769017910	Jul 13, 2019 (153)
50	PACBIO	ss3786370623	Jul 13, 2019 (153)
51	PACBIO	ss3791593794	Jul 13, 2019 (153)
52	PACBIO	ss3796475508	Jul 13, 2019 (153)
53	KHV_HUMAN_GENOMES	ss3812175718	Jul 13, 2019 (153)
54	EVA	ss3831579981	Apr 26, 2020 (154)
55	EVA	ss3839306278	Apr 26, 2020 (154)
56	EVA	ss3844768856	Apr 26, 2020 (154)
57	SGDP_PRJ	ss3871696032	Apr 26, 2020 (154)
58	KRGDB	ss3919351384	Apr 26, 2020 (154)
59	KOGIC	ss3965451050	Apr 26, 2020 (154)
60	TOPMED	ss4815515659	Apr 26, 2021 (155)
61	TOMMO_GENOMICS	ss5192449615	Apr 26, 2021 (155)
62	1000G_HIGH_COVERAGE	ss5280081321	Oct 13, 2022 (156)
63	EVA	ss5386557230	Oct 13, 2022 (156)
64	HUGCELL_USP	ss5476329611	Oct 13, 2022 (156)
65	1000G_HIGH_COVERAGE	ss5572000591	Oct 13, 2022 (156)
66	SANFORD_IMAGENETICS	ss5647072981	Oct 13, 2022 (156)
67	TOMMO_GENOMICS	ss5735601972	Oct 13, 2022 (156)
68	YY_MCH	ss5810414980	Oct 13, 2022 (156)
69	EVA	ss5828961131	Oct 13, 2022 (156)
70	EVA	ss5856706090	Oct 13, 2022 (156)
71	EVA	ss5915854555	Oct 13, 2022 (156)
72	EVA	ss5976348745	Oct 13, 2022 (156)
73	1000Genomes	NC_000009.11 - 20177209	Oct 12, 2018 (152)
74	1000Genomes_30x	NC_000009.12 - 20177211	Oct 13, 2022 (156)
75	The Avon Longitudinal Study of Parents and Children	NC_000009.11 - 20177209	Oct 12, 2018 (152)
76	The Danish reference pan genome	NC_000009.11 - 20177209	Apr 26, 2020 (154)
77	gnomAD - Genomes	NC_000009.12 - 20177211	Apr 26, 2021 (155)
78	Genome of the Netherlands Release 5	NC_000009.11 - 20177209	Apr 26, 2020 (154)
79	KOREAN population from KRGDB	NC_000009.11 - 20177209	Apr 26, 2020 (154)
80	Korean Genome Project	NC_000009.12 - 20177211	Apr 26, 2020 (154)
81	Northern Sweden	NC_000009.11 - 20177209	Jul 13, 2019 (153)
82	Qatari	NC_000009.11 - 20177209	Apr 26, 2020 (154)
83	SGDP_PRJ	NC_000009.11 - 20177209	Apr 26, 2020 (154)
84	Siberian	NC_000009.11 - 20177209	Apr 26, 2020 (154)
85	8.3KJPN	NC_000009.11 - 20177209	Apr 26, 2021 (155)
86	14KJPN	NC_000009.12 - 20177211	Oct 13, 2022 (156)
87	TopMed	NC_000009.12 - 20177211	Apr 26, 2021 (155)
88	UK 10K study - Twins	NC_000009.11 - 20177209	Oct 12, 2018 (152)
89	ALFA	NC_000009.12 - 20177211	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)
rs58570811	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
26528778, ss3919351384	NC_000009.11:20177208:C:A	NC_000009.12:20177210:C:A	(self)
ss77822423, ss86198915	NC_000009.9:20167208:C:T	NC_000009.12:20177210:C:T	(self)
ss94026395, ss108662018, ss114278146, ss115705733, ss164732724, ss200202452, ss206698671, ss280143283, ss285985771, ss294413864	NC_000009.10:20167208:C:T	NC_000009.12:20177210:C:T	(self)
45472858, 25295298, 9188273, 11283963, 26528778, 9665958, 11723945, 23713012, 6295722, 50418922, 25295298, ss224168305, ss234759323, ss241545547, ss655724760, ss986398302, ss1076181529, ss1333235363, ss1431778213, ss1583023336, ss1622423964, ss1665417997, ss1805917375, ss1929682015, ss1971175208, ss2025553190, ss2153779368, ss2627250682, ss2709582427, ss2876357219, ss3004512968, ss3348563478, ss3736381093, ss3769017910, ss3786370623, ss3791593794, ss3796475508, ss3831579981, ss3839306278, ss3871696032, ss3919351384, ss5192449615, ss5386557230, ss5647072981, ss5828961131, ss5976348745	NC_000009.11:20177208:C:T	NC_000009.12:20177210:C:T	(self)
59526526, 320494562, 21829051, 69439076, 652893220, 2659731299, ss2310083819, ss3026566550, ss3649090332, ss3723633074, ss3812175718, ss3844768856, ss3965451050, ss4815515659, ss5280081321, ss5476329611, ss5572000591, ss5735601972, ss5810414980, ss5856706090, ss5915854555	NC_000009.12:20177210:C:T	NC_000009.12:20177210:C:T	(self)
ss11274917	NT_008413.15:20167209:C:T	NC_000009.12:20177210:C:T	(self)
ss15539534, ss19796669, ss22782923	NT_008413.16:20167208:C:T	NC_000009.12:20177210:C:T	(self)
ss43433570, ss97713066, ss105668388, ss134186037, ss144004743, ss157284925	NT_008413.18:20167208:C:T	NC_000009.12:20177210: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 rs7466134

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

rs7466134