Name: rs1543334
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.

rs1543334

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:10334286 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.182020 (48179/264690, TOPMED)
C=0.194106 (27204/140150, GnomAD)
C=0.15593 (12272/78700, PAGE_STUDY) (+ 16 more)
C=0.22015 (6836/31052, ALFA)
C=0.32826 (9276/28258, 14KJPN)
C=0.32953 (5523/16760, 8.3KJPN)
C=0.1858 (1190/6404, 1000G_30x)
C=0.1905 (954/5008, 1000G)
C=0.2580 (1156/4480, Estonian)
C=0.2122 (818/3854, ALSPAC)
C=0.2206 (818/3708, TWINSUK)
C=0.3778 (1107/2930, KOREAN)
C=0.229 (229/998, GoNL)
C=0.195 (117/600, NorthernSweden)
C=0.315 (68/216, Qatari)
C=0.350 (75/214, Vietnamese)
A=0.448 (95/212, SGDP_PRJ)
C=0.23 (9/40, GENOME_DK)
A=0.47 (17/36, 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	31052	A=0.77985	C=0.22015
European	Sub	24818	A=0.76275	C=0.23725
African	Sub	3176	A=0.8933	C=0.1067
African Others	Sub	124	A=0.871	C=0.129
African American	Sub	3052	A=0.8942	C=0.1058
Asian	Sub	162	A=0.617	C=0.383
East Asian	Sub	134	A=0.597	C=0.403
Other Asian	Sub	28	A=0.71	C=0.29
Latin American 1	Sub	168	A=0.815	C=0.185
Latin American 2	Sub	700	A=0.860	C=0.140
South Asian	Sub	120	A=0.858	C=0.142
Other	Sub	1908	A=0.7898	C=0.2102

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=0.817980	C=0.182020
gnomAD - Genomes	Global	Study-wide	140150	A=0.805894	C=0.194106
gnomAD - Genomes	European	Sub	75868	A=0.75767	C=0.24233
gnomAD - Genomes	African	Sub	42026	A=0.89359	C=0.10641
gnomAD - Genomes	American	Sub	13652	A=0.84771	C=0.15229
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.7684	C=0.2316
gnomAD - Genomes	East Asian	Sub	3130	A=0.6527	C=0.3473
gnomAD - Genomes	Other	Sub	2150	A=0.8088	C=0.1912
The PAGE Study	Global	Study-wide	78700	A=0.84407	C=0.15593
The PAGE Study	AfricanAmerican	Sub	32516	A=0.88972	C=0.11028
The PAGE Study	Mexican	Sub	10808	A=0.87398	C=0.12602
The PAGE Study	Asian	Sub	8318	A=0.6760	C=0.3240
The PAGE Study	PuertoRican	Sub	7918	A=0.8402	C=0.1598
The PAGE Study	NativeHawaiian	Sub	4534	A=0.7788	C=0.2212
The PAGE Study	Cuban	Sub	4230	A=0.7974	C=0.2026
The PAGE Study	Dominican	Sub	3828	A=0.8365	C=0.1635
The PAGE Study	CentralAmerican	Sub	2450	A=0.8853	C=0.1147
The PAGE Study	SouthAmerican	Sub	1982	A=0.8824	C=0.1176
The PAGE Study	NativeAmerican	Sub	1260	A=0.8198	C=0.1802
The PAGE Study	SouthAsian	Sub	856	A=0.840	C=0.160
Allele Frequency Aggregator	Total	Global	31052	A=0.77985	C=0.22015
Allele Frequency Aggregator	European	Sub	24818	A=0.76275	C=0.23725
Allele Frequency Aggregator	African	Sub	3176	A=0.8933	C=0.1067
Allele Frequency Aggregator	Other	Sub	1908	A=0.7898	C=0.2102
Allele Frequency Aggregator	Latin American 2	Sub	700	A=0.860	C=0.140
Allele Frequency Aggregator	Latin American 1	Sub	168	A=0.815	C=0.185
Allele Frequency Aggregator	Asian	Sub	162	A=0.617	C=0.383
Allele Frequency Aggregator	South Asian	Sub	120	A=0.858	C=0.142
14KJPN	JAPANESE	Study-wide	28258	A=0.67174	C=0.32826
8.3KJPN	JAPANESE	Study-wide	16760	A=0.67047	C=0.32953
1000Genomes_30x	Global	Study-wide	6404	A=0.8142	C=0.1858
1000Genomes_30x	African	Sub	1786	A=0.8998	C=0.1002
1000Genomes_30x	Europe	Sub	1266	A=0.7828	C=0.2172
1000Genomes_30x	South Asian	Sub	1202	A=0.8527	C=0.1473
1000Genomes_30x	East Asian	Sub	1170	A=0.6368	C=0.3632
1000Genomes_30x	American	Sub	980	A=0.863	C=0.137
1000Genomes	Global	Study-wide	5008	A=0.8095	C=0.1905
1000Genomes	African	Sub	1322	A=0.9032	C=0.0968
1000Genomes	East Asian	Sub	1008	A=0.6369	C=0.3631
1000Genomes	Europe	Sub	1006	A=0.7753	C=0.2247
1000Genomes	South Asian	Sub	978	A=0.856	C=0.144
1000Genomes	American	Sub	694	A=0.866	C=0.134
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.7420	C=0.2580
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.7878	C=0.2122
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.7794	C=0.2206
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.6222	C=0.3778
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.771	C=0.229
Northern Sweden	ACPOP	Study-wide	600	A=0.805	C=0.195
Qatari	Global	Study-wide	216	A=0.685	C=0.315
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.650	C=0.350
SGDP_PRJ	Global	Study-wide	212	A=0.448	C=0.552
The Danish reference pan genome	Danish	Study-wide	40	A=0.78	C=0.23
Siberian	Global	Study-wide	36	A=0.47	C=0.53

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 20	NC_000020.11:g.10334286A>C
GRCh37.p13 chr 20	NC_000020.10:g.10314934A>C
HIGD1AP15 pseudogene	NG_032775.2:g.34A>C

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=	C
GRCh38.p14 chr 20	NC_000020.11:g.10334286=	NC_000020.11:g.10334286A>C
GRCh37.p13 chr 20	NC_000020.10:g.10314934=	NC_000020.10:g.10314934A>C
HIGD1AP15 pseudogene	NG_032775.2:g.34=	NG_032775.2:g.34A>C

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#.

73 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2385390	Oct 23, 2000 (88)
2	ABI	ss41387210	Mar 15, 2006 (126)
3	HGSV	ss84184531	Dec 16, 2007 (130)
4	BGI	ss103727083	Dec 01, 2009 (131)
5	1000GENOMES	ss111719994	Jan 25, 2009 (130)
6	IGMI-SNU	ss115461903	Feb 06, 2009 (130)
7	GMI	ss156162436	Dec 01, 2009 (131)
8	BCM-HGSC-SUB	ss208682448	Jul 04, 2010 (132)
9	1000GENOMES	ss228256465	Jul 14, 2010 (132)
10	1000GENOMES	ss237762530	Jul 15, 2010 (132)
11	1000GENOMES	ss243949094	Jul 15, 2010 (132)
12	GMI	ss283299888	May 04, 2012 (137)
13	ILLUMINA	ss479192406	May 04, 2012 (137)
14	ILLUMINA	ss484156869	May 04, 2012 (137)
15	ILLUMINA	ss532783311	Sep 08, 2015 (146)
16	TISHKOFF	ss566135690	Apr 25, 2013 (138)
17	SSMP	ss662006660	Apr 25, 2013 (138)
18	ILLUMINA	ss779540835	Aug 21, 2014 (142)
19	ILLUMINA	ss780920164	Aug 21, 2014 (142)
20	ILLUMINA	ss835011571	Aug 21, 2014 (142)
21	EVA-GONL	ss994538651	Aug 21, 2014 (142)
22	JMKIDD_LAB	ss1082073060	Aug 21, 2014 (142)
23	1000GENOMES	ss1364063921	Aug 21, 2014 (142)
24	DDI	ss1428995667	Apr 01, 2015 (144)
25	EVA_GENOME_DK	ss1579436948	Apr 01, 2015 (144)
26	EVA_UK10K_ALSPAC	ss1638411950	Apr 01, 2015 (144)
27	EVA_UK10K_TWINSUK	ss1681405983	Apr 01, 2015 (144)
28	EVA_DECODE	ss1698594603	Apr 01, 2015 (144)
29	WEILL_CORNELL_DGM	ss1938049107	Feb 12, 2016 (147)
30	ILLUMINA	ss1959898782	Feb 12, 2016 (147)
31	JJLAB	ss2029803811	Sep 14, 2016 (149)
32	USC_VALOUEV	ss2158357533	Dec 20, 2016 (150)
33	HUMAN_LONGEVITY	ss2241325242	Dec 20, 2016 (150)
34	SYSTEMSBIOZJU	ss2629398995	Nov 08, 2017 (151)
35	ILLUMINA	ss2633777280	Nov 08, 2017 (151)
36	GRF	ss2704030817	Nov 08, 2017 (151)
37	GNOMAD	ss2965430351	Nov 08, 2017 (151)
38	SWEGEN	ss3017867514	Nov 08, 2017 (151)
39	ILLUMINA	ss3022100954	Nov 08, 2017 (151)
40	BIOINF_KMB_FNS_UNIBA	ss3028734889	Nov 08, 2017 (151)
41	CSHL	ss3352419156	Nov 08, 2017 (151)
42	ILLUMINA	ss3628351183	Oct 12, 2018 (152)
43	ILLUMINA	ss3631735043	Oct 12, 2018 (152)
44	ILLUMINA	ss3642173402	Oct 12, 2018 (152)
45	ILLUMINA	ss3652555370	Oct 12, 2018 (152)
46	EGCUT_WGS	ss3684584542	Jul 13, 2019 (153)
47	EVA_DECODE	ss3706559164	Jul 13, 2019 (153)
48	ILLUMINA	ss3725900123	Jul 13, 2019 (153)
49	ACPOP	ss3743248664	Jul 13, 2019 (153)
50	EVA	ss3758421386	Jul 13, 2019 (153)
51	PAGE_CC	ss3772036622	Jul 13, 2019 (153)
52	KHV_HUMAN_GENOMES	ss3821595167	Jul 13, 2019 (153)
53	EVA	ss3835587837	Apr 27, 2020 (154)
54	SGDP_PRJ	ss3888731962	Apr 27, 2020 (154)
55	KRGDB	ss3938920749	Apr 27, 2020 (154)
56	TOPMED	ss5082256916	Apr 27, 2021 (155)
57	TOMMO_GENOMICS	ss5228839596	Apr 27, 2021 (155)
58	1000G_HIGH_COVERAGE	ss5308085118	Oct 13, 2022 (156)
59	EVA	ss5315994795	Oct 13, 2022 (156)
60	EVA	ss5436259906	Oct 13, 2022 (156)
61	HUGCELL_USP	ss5500485663	Oct 13, 2022 (156)
62	1000G_HIGH_COVERAGE	ss5614165958	Oct 13, 2022 (156)
63	SANFORD_IMAGENETICS	ss5624480696	Oct 13, 2022 (156)
64	SANFORD_IMAGENETICS	ss5662864828	Oct 13, 2022 (156)
65	TOMMO_GENOMICS	ss5787827480	Oct 13, 2022 (156)
66	YY_MCH	ss5817816054	Oct 13, 2022 (156)
67	EVA	ss5845444067	Oct 13, 2022 (156)
68	EVA	ss5847502468	Oct 13, 2022 (156)
69	EVA	ss5853068821	Oct 13, 2022 (156)
70	EVA	ss5922673916	Oct 13, 2022 (156)
71	EVA	ss5957766296	Oct 13, 2022 (156)
72	EVA	ss5979610314	Oct 13, 2022 (156)
73	EVA	ss5981076598	Oct 13, 2022 (156)
74	1000Genomes	NC_000020.10 - 10314934	Oct 12, 2018 (152)
75	1000Genomes_30x	NC_000020.11 - 10334286	Oct 13, 2022 (156)
76	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 10314934	Oct 12, 2018 (152)
77	Genetic variation in the Estonian population	NC_000020.10 - 10314934	Oct 12, 2018 (152)
78	The Danish reference pan genome	NC_000020.10 - 10314934	Apr 27, 2020 (154)
79	gnomAD - Genomes	NC_000020.11 - 10334286	Apr 27, 2021 (155)
80	Genome of the Netherlands Release 5	NC_000020.10 - 10314934	Apr 27, 2020 (154)
81	KOREAN population from KRGDB	NC_000020.10 - 10314934	Apr 27, 2020 (154)
82	Northern Sweden	NC_000020.10 - 10314934	Jul 13, 2019 (153)
83	The PAGE Study	NC_000020.11 - 10334286	Jul 13, 2019 (153)
84	Qatari	NC_000020.10 - 10314934	Apr 27, 2020 (154)
85	SGDP_PRJ	NC_000020.10 - 10314934	Apr 27, 2020 (154)
86	Siberian	NC_000020.10 - 10314934	Apr 27, 2020 (154)
87	8.3KJPN	NC_000020.10 - 10314934	Apr 27, 2021 (155)
88	14KJPN	NC_000020.11 - 10334286	Oct 13, 2022 (156)
89	TopMed	NC_000020.11 - 10334286	Apr 27, 2021 (155)
90	UK 10K study - Twins	NC_000020.10 - 10314934	Oct 12, 2018 (152)
91	A Vietnamese Genetic Variation Database	NC_000020.10 - 10314934	Jul 13, 2019 (153)
92	ALFA	NC_000020.11 - 10334286	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)
rs61098911	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss84184531, ss111719994, ss208682448, ss283299888, ss484156869, ss1698594603	NC_000020.9:10262933:A:C	NC_000020.11:10334285:A:C	(self)
77503362, 42904447, 30322790, 5601887, 19116765, 46098143, 16533529, 20091029, 40748942, 10873887, 86808903, 42904447, 9471967, ss228256465, ss237762530, ss243949094, ss479192406, ss532783311, ss566135690, ss662006660, ss779540835, ss780920164, ss835011571, ss994538651, ss1082073060, ss1364063921, ss1428995667, ss1579436948, ss1638411950, ss1681405983, ss1938049107, ss1959898782, ss2029803811, ss2158357533, ss2629398995, ss2633777280, ss2704030817, ss2965430351, ss3017867514, ss3022100954, ss3352419156, ss3628351183, ss3631735043, ss3642173402, ss3652555370, ss3684584542, ss3743248664, ss3758421386, ss3835587837, ss3888731962, ss3938920749, ss5228839596, ss5315994795, ss5436259906, ss5624480696, ss5662864828, ss5845444067, ss5847502468, ss5957766296, ss5979610314, ss5981076598	NC_000020.10:10314933:A:C	NC_000020.11:10334285:A:C	(self)
101691893, 546477195, 1258091, 121664584, 357365861, 3819216062, ss2241325242, ss3028734889, ss3706559164, ss3725900123, ss3772036622, ss3821595167, ss5082256916, ss5308085118, ss5500485663, ss5614165958, ss5787827480, ss5817816054, ss5853068821, ss5922673916	NC_000020.11:10334285:A:C	NC_000020.11:10334285:A:C	(self)
ss2385390, ss41387210, ss103727083, ss115461903, ss156162436	NT_011387.8:10254933:A:C	NC_000020.11:10334285:A: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 rs1543334

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1543334