Name: rs471054
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.

rs471054

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:49896699 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.399139 (105648/264690, TOPMED)
T=0.402651 (56384/140032, GnomAD)
C=0.15422 (4358/28258, 14KJPN) (+ 18 more)
T=0.36049 (6222/17260, ALFA)
C=0.15531 (2603/16760, 8.3KJPN)
T=0.4775 (3058/6404, 1000G_30x)
T=0.4874 (2441/5008, 1000G)
C=0.4286 (1920/4480, Estonian)
T=0.4766 (1837/3854, ALSPAC)
T=0.4787 (1775/3708, TWINSUK)
C=0.1867 (547/2930, KOREAN)
T=0.4274 (807/1888, HapMap)
C=0.1823 (334/1832, Korea1K)
T=0.471 (470/998, GoNL)
C=0.470 (282/600, NorthernSweden)
C=0.245 (108/440, SGDP_PRJ)
T=0.468 (101/216, Qatari)
C=0.266 (57/214, Vietnamese)
C=0.19 (9/48, Siberian)
C=0.50 (20/40, GENOME_DK)
T=0.50 (20/40, GENOME_DK)

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	17260	C=0.63951	G=0.00000, T=0.36049
European	Sub	13196	C=0.56790	G=0.00000, T=0.43210
African	Sub	3354	C=0.9070	G=0.0000, T=0.0930
African Others	Sub	140	C=0.964	G=0.000, T=0.036
African American	Sub	3214	C=0.9045	G=0.0000, T=0.0955
Asian	Sub	30	C=0.73	G=0.00, T=0.27
East Asian	Sub	24	C=0.71	G=0.00, T=0.29
Other Asian	Sub	6	C=0.8	G=0.0, T=0.2
Latin American 1	Sub	62	C=0.90	G=0.00, T=0.10
Latin American 2	Sub	144	C=0.778	G=0.000, T=0.222
South Asian	Sub	12	C=0.75	G=0.00, T=0.25
Other	Sub	462	C=0.656	G=0.000, T=0.344

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.600861	T=0.399139
gnomAD - Genomes	Global	Study-wide	140032	C=0.597349	T=0.402651
gnomAD - Genomes	European	Sub	75822	C=0.51076	T=0.48924
gnomAD - Genomes	African	Sub	41976	C=0.83271	T=0.16729
gnomAD - Genomes	American	Sub	13630	C=0.44204	T=0.55796
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.6183	T=0.3817
gnomAD - Genomes	East Asian	Sub	3132	C=0.2219	T=0.7781
gnomAD - Genomes	Other	Sub	2150	C=0.5549	T=0.4451
14KJPN	JAPANESE	Study-wide	28258	C=0.15422	T=0.84578
Allele Frequency Aggregator	Total	Global	17260	C=0.63951	G=0.00000, T=0.36049
Allele Frequency Aggregator	European	Sub	13196	C=0.56790	G=0.00000, T=0.43210
Allele Frequency Aggregator	African	Sub	3354	C=0.9070	G=0.0000, T=0.0930
Allele Frequency Aggregator	Other	Sub	462	C=0.656	G=0.000, T=0.344
Allele Frequency Aggregator	Latin American 2	Sub	144	C=0.778	G=0.000, T=0.222
Allele Frequency Aggregator	Latin American 1	Sub	62	C=0.90	G=0.00, T=0.10
Allele Frequency Aggregator	Asian	Sub	30	C=0.73	G=0.00, T=0.27
Allele Frequency Aggregator	South Asian	Sub	12	C=0.75	G=0.00, T=0.25
8.3KJPN	JAPANESE	Study-wide	16760	C=0.15531	T=0.84469
1000Genomes_30x	Global	Study-wide	6404	C=0.5225	T=0.4775
1000Genomes_30x	African	Sub	1786	C=0.8819	T=0.1181
1000Genomes_30x	Europe	Sub	1266	C=0.5458	T=0.4542
1000Genomes_30x	South Asian	Sub	1202	C=0.3411	T=0.6589
1000Genomes_30x	East Asian	Sub	1170	C=0.2265	T=0.7735
1000Genomes_30x	American	Sub	980	C=0.413	T=0.587
1000Genomes	Global	Study-wide	5008	C=0.5126	T=0.4874
1000Genomes	African	Sub	1322	C=0.8790	T=0.1210
1000Genomes	East Asian	Sub	1008	C=0.2282	T=0.7718
1000Genomes	Europe	Sub	1006	C=0.5517	T=0.4483
1000Genomes	South Asian	Sub	978	C=0.339	T=0.661
1000Genomes	American	Sub	694	C=0.415	T=0.585
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.4286	T=0.5714
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.5234	T=0.4766
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.5213	T=0.4787
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.1867	T=0.8133
HapMap	Global	Study-wide	1888	C=0.5726	T=0.4274
HapMap	American	Sub	768	C=0.470	T=0.530
HapMap	African	Sub	690	C=0.819	T=0.181
HapMap	Asian	Sub	254	C=0.161	T=0.839
HapMap	Europe	Sub	176	C=0.648	T=0.352
Korean Genome Project	KOREAN	Study-wide	1832	C=0.1823	T=0.8177
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.529	T=0.471
Northern Sweden	ACPOP	Study-wide	600	C=0.470	T=0.530
SGDP_PRJ	Global	Study-wide	440	C=0.245	T=0.755
Qatari	Global	Study-wide	216	C=0.532	T=0.468
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.266	T=0.734
Siberian	Global	Study-wide	48	C=0.19	T=0.81
The Danish reference pan genome	Danish	Study-wide	40	C=0.50	T=0.50

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.49896699C>G
GRCh38.p14 chr 20	NC_000020.11:g.49896699C>T
GRCh37.p13 chr 20	NC_000020.10:g.48513236C>G
GRCh37.p13 chr 20	NC_000020.10:g.48513236C>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	C=	G	T
GRCh38.p14 chr 20	NC_000020.11:g.49896699=	NC_000020.11:g.49896699C>G	NC_000020.11:g.49896699C>T
GRCh37.p13 chr 20	NC_000020.10:g.48513236=	NC_000020.10:g.48513236C>G	NC_000020.10:g.48513236C>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#.

83 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss640396	Aug 11, 2000 (83)
2	SC	ss4323650	Mar 26, 2002 (111)
3	SC_SNP	ss8384555	Apr 21, 2003 (117)
4	SSAHASNP	ss21767237	Apr 05, 2004 (121)
5	ABI	ss41365575	Mar 15, 2006 (126)
6	ILLUMINA	ss74970881	Dec 05, 2007 (129)
7	BCMHGSC_JDW	ss91719061	Mar 24, 2008 (129)
8	HUMANGENOME_JCVI	ss96199844	Feb 05, 2009 (130)
9	BGI	ss103766458	Dec 01, 2009 (131)
10	1000GENOMES	ss112070114	Jan 25, 2009 (130)
11	IGMI-SNU	ss115479030	Feb 05, 2009 (130)
12	ILLUMINA-UK	ss117568371	Feb 14, 2009 (130)
13	KRIBB_YJKIM	ss119354655	Dec 01, 2009 (131)
14	ENSEMBL	ss135698217	Dec 01, 2009 (131)
15	ENSEMBL	ss138254105	Dec 01, 2009 (131)
16	GMI	ss156498858	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss168245753	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss172135094	Jul 04, 2010 (132)
19	ILLUMINA	ss173786902	Jul 04, 2010 (132)
20	1000GENOMES	ss228388996	Jul 14, 2010 (132)
21	1000GENOMES	ss237857049	Jul 15, 2010 (132)
22	1000GENOMES	ss244024021	Jul 15, 2010 (132)
23	BL	ss255690388	May 09, 2011 (134)
24	GMI	ss283406601	May 04, 2012 (137)
25	GMI	ss287467948	Apr 25, 2013 (138)
26	PJP	ss292574604	May 09, 2011 (134)
27	TISHKOFF	ss566294927	Apr 25, 2013 (138)
28	SSMP	ss662175875	Apr 25, 2013 (138)
29	EVA-GONL	ss994794822	Aug 21, 2014 (142)
30	JMKIDD_LAB	ss1082257325	Aug 21, 2014 (142)
31	1000GENOMES	ss1365063234	Aug 21, 2014 (142)
32	DDI	ss1429074347	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1579533401	Apr 01, 2015 (144)
34	EVA_UK10K_ALSPAC	ss1638934469	Apr 01, 2015 (144)
35	EVA_UK10K_TWINSUK	ss1681928502	Apr 01, 2015 (144)
36	EVA_DECODE	ss1698855945	Apr 01, 2015 (144)
37	EVA_SVP	ss1713699593	Apr 01, 2015 (144)
38	HAMMER_LAB	ss1809533776	Sep 08, 2015 (146)
39	WEILL_CORNELL_DGM	ss1938310659	Feb 12, 2016 (147)
40	GENOMED	ss1969147836	Jul 19, 2016 (147)
41	JJLAB	ss2029935060	Sep 14, 2016 (149)
42	USC_VALOUEV	ss2158504661	Dec 20, 2016 (150)
43	HUMAN_LONGEVITY	ss2243356502	Dec 20, 2016 (150)
44	SYSTEMSBIOZJU	ss2629461650	Nov 08, 2017 (151)
45	GRF	ss2704199513	Nov 08, 2017 (151)
46	GNOMAD	ss2968247089	Nov 08, 2017 (151)
47	SWEGEN	ss3018300114	Nov 08, 2017 (151)
48	BIOINF_KMB_FNS_UNIBA	ss3028800443	Nov 08, 2017 (151)
49	CSHL	ss3352543359	Nov 08, 2017 (151)
50	ILLUMINA	ss3638350470	Oct 12, 2018 (152)
51	ILLUMINA	ss3641128989	Oct 12, 2018 (152)
52	ILLUMINA	ss3641425227	Oct 12, 2018 (152)
53	ILLUMINA	ss3643312872	Oct 12, 2018 (152)
54	URBANLAB	ss3651034320	Oct 12, 2018 (152)
55	EGCUT_WGS	ss3684984925	Jul 13, 2019 (153)
56	EVA_DECODE	ss3707091273	Jul 13, 2019 (153)
57	ACPOP	ss3743455159	Jul 13, 2019 (153)
58	EVA	ss3758734207	Jul 13, 2019 (153)
59	PACBIO	ss3788666413	Jul 13, 2019 (153)
60	PACBIO	ss3793554354	Jul 13, 2019 (153)
61	PACBIO	ss3798441351	Jul 13, 2019 (153)
62	KHV_HUMAN_GENOMES	ss3821892108	Jul 13, 2019 (153)
63	EVA	ss3835707992	Apr 27, 2020 (154)
64	EVA	ss3841477985	Apr 27, 2020 (154)
65	EVA	ss3846991067	Apr 27, 2020 (154)
66	SGDP_PRJ	ss3889253806	Apr 27, 2020 (154)
67	KRGDB	ss3939560609	Apr 27, 2020 (154)
68	KOGIC	ss3982432706	Apr 27, 2020 (154)
69	EVA	ss4017852013	Apr 27, 2021 (155)
70	TOPMED	ss5091142639	Apr 27, 2021 (155)
71	TOMMO_GENOMICS	ss5229985202	Apr 27, 2021 (155)
72	1000G_HIGH_COVERAGE	ss5309057600	Oct 16, 2022 (156)
73	EVA	ss5437877291	Oct 16, 2022 (156)
74	HUGCELL_USP	ss5501310453	Oct 16, 2022 (156)
75	EVA	ss5512238559	Oct 16, 2022 (156)
76	1000G_HIGH_COVERAGE	ss5615639523	Oct 16, 2022 (156)
77	SANFORD_IMAGENETICS	ss5663356065	Oct 16, 2022 (156)
78	TOMMO_GENOMICS	ss5789892918	Oct 16, 2022 (156)
79	YY_MCH	ss5818108820	Oct 16, 2022 (156)
80	EVA	ss5845792837	Oct 16, 2022 (156)
81	EVA	ss5853171835	Oct 16, 2022 (156)
82	EVA	ss5923724460	Oct 16, 2022 (156)
83	EVA	ss5958280640	Oct 16, 2022 (156)
84	1000Genomes	NC_000020.10 - 48513236	Oct 12, 2018 (152)
85	1000Genomes_30x	NC_000020.11 - 49896699	Oct 16, 2022 (156)
86	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 48513236	Oct 12, 2018 (152)
87	Genetic variation in the Estonian population	NC_000020.10 - 48513236	Oct 12, 2018 (152)
88	The Danish reference pan genome	NC_000020.10 - 48513236	Apr 27, 2020 (154)
89	gnomAD - Genomes	NC_000020.11 - 49896699	Apr 27, 2021 (155)
90	Genome of the Netherlands Release 5	NC_000020.10 - 48513236	Apr 27, 2020 (154)
91	HapMap	NC_000020.11 - 49896699	Apr 27, 2020 (154)
92	KOREAN population from KRGDB	NC_000020.10 - 48513236	Apr 27, 2020 (154)
93	Korean Genome Project	NC_000020.11 - 49896699	Apr 27, 2020 (154)
94	Northern Sweden	NC_000020.10 - 48513236	Jul 13, 2019 (153)
95	Qatari	NC_000020.10 - 48513236	Apr 27, 2020 (154)
96	SGDP_PRJ	NC_000020.10 - 48513236	Apr 27, 2020 (154)
97	Siberian	NC_000020.10 - 48513236	Apr 27, 2020 (154)
98	8.3KJPN	NC_000020.10 - 48513236	Apr 27, 2021 (155)
99	14KJPN	NC_000020.11 - 49896699	Oct 16, 2022 (156)
100	TopMed	NC_000020.11 - 49896699	Apr 27, 2021 (155)
101	UK 10K study - Twins	NC_000020.10 - 48513236	Oct 12, 2018 (152)
102	A Vietnamese Genetic Variation Database	NC_000020.10 - 48513236	Jul 13, 2019 (153)
103	ALFA	NC_000020.11 - 49896699	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)
rs3091530	Feb 20, 2003 (111)
rs6067262	Aug 27, 2003 (117)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
5442336789	NC_000020.11:49896698:C:G	NC_000020.11:49896698:C:G	(self)
ss91719061, ss112070114, ss117568371, ss168245753, ss172135094, ss255690388, ss283406601, ss287467948, ss292574604, ss1698855945, ss1713699593, ss3643312872	NC_000020.9:47946642:C:T	NC_000020.11:49896698:C:T	(self)
78536513, 43477300, 30723173, 5698340, 19365598, 46738003, 16740024, 20352581, 41270786, 11021015, 87954509, 43477300, 9591203, ss228388996, ss237857049, ss244024021, ss566294927, ss662175875, ss994794822, ss1082257325, ss1365063234, ss1429074347, ss1579533401, ss1638934469, ss1681928502, ss1809533776, ss1938310659, ss1969147836, ss2029935060, ss2158504661, ss2629461650, ss2704199513, ss2968247089, ss3018300114, ss3352543359, ss3638350470, ss3641128989, ss3641425227, ss3684984925, ss3743455159, ss3758734207, ss3788666413, ss3793554354, ss3798441351, ss3835707992, ss3841477985, ss3889253806, ss3939560609, ss4017852013, ss5229985202, ss5437877291, ss5512238559, ss5663356065, ss5845792837, ss5958280640	NC_000020.10:48513235:C:T	NC_000020.11:49896698:C:T	(self)
103165458, 553969069, 2140459, 38810707, 123730022, 366251584, 5442336789, ss2243356502, ss3028800443, ss3651034320, ss3707091273, ss3821892108, ss3846991067, ss3982432706, ss5091142639, ss5309057600, ss5501310453, ss5615639523, ss5789892918, ss5818108820, ss5853171835, ss5923724460	NC_000020.11:49896698:C:T	NC_000020.11:49896698:C:T	(self)
ss21767237	NT_011362.8:13566143:C:T	NC_000020.11:49896698:C:T	(self)
ss640396, ss4323650, ss8384555, ss41365575, ss74970881, ss96199844, ss103766458, ss115479030, ss119354655, ss135698217, ss138254105, ss156498858, ss173786902	NT_011362.10:18709327:C:T	NC_000020.11:49896698: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 rs471054

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

rs471054