Name: rs471074
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.

rs471074

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:116685595 (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>A / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.136888 (36233/264690, TOPMED)
T=0.49756 (14059/28256, 14KJPN)
T=0.49988 (8378/16760, 8.3KJPN) (+ 15 more)
T=0.1655 (1204/7276, ALFA)
T=0.1783 (1142/6404, 1000G_30x)
T=0.1829 (916/5008, 1000G)
T=0.1319 (591/4480, Estonian)
T=0.1733 (668/3854, ALSPAC)
T=0.1564 (580/3708, TWINSUK)
T=0.4321 (1266/2930, KOREAN)
T=0.4279 (784/1832, Korea1K)
T=0.166 (166/998, GoNL)
T=0.115 (69/600, NorthernSweden)
T=0.169 (84/496, SGDP_PRJ)
T=0.162 (35/216, Qatari)
G=0.468 (101/216, Vietnamese)
T=0.24 (13/54, Siberian)
T=0.15 (6/40, 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	7276	T=0.1655	A=0.0000, G=0.8345
European	Sub	6850	T=0.1604	A=0.0000, G=0.8396
African	Sub	138	T=0.072	A=0.000, G=0.928
African Others	Sub	6	T=0.0	A=0.0, G=1.0
African American	Sub	132	T=0.076	A=0.000, G=0.924
Asian	Sub	30	T=0.87	A=0.00, G=0.13
East Asian	Sub	22	T=0.91	A=0.00, G=0.09
Other Asian	Sub	8	T=0.8	A=0.0, G=0.2
Latin American 1	Sub	2	T=1.0	A=0.0, G=0.0
Latin American 2	Sub	18	T=1.00	A=0.00, G=0.00
South Asian	Sub	4	T=0.2	A=0.0, G=0.8
Other	Sub	234	T=0.205	A=0.000, G=0.795

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=0.136888	G=0.863112
14KJPN	JAPANESE	Study-wide	28256	T=0.49756	G=0.50244
8.3KJPN	JAPANESE	Study-wide	16760	T=0.49988	G=0.50012
Allele Frequency Aggregator	Total	Global	7276	T=0.1655	A=0.0000, G=0.8345
Allele Frequency Aggregator	European	Sub	6850	T=0.1604	A=0.0000, G=0.8396
Allele Frequency Aggregator	Other	Sub	234	T=0.205	A=0.000, G=0.795
Allele Frequency Aggregator	African	Sub	138	T=0.072	A=0.000, G=0.928
Allele Frequency Aggregator	Asian	Sub	30	T=0.87	A=0.00, G=0.13
Allele Frequency Aggregator	Latin American 2	Sub	18	T=1.00	A=0.00, G=0.00
Allele Frequency Aggregator	South Asian	Sub	4	T=0.2	A=0.0, G=0.8
Allele Frequency Aggregator	Latin American 1	Sub	2	T=1.0	A=0.0, G=0.0
1000Genomes_30x	Global	Study-wide	6404	T=0.1783	G=0.8217
1000Genomes_30x	African	Sub	1786	T=0.0269	G=0.9731
1000Genomes_30x	Europe	Sub	1266	T=0.1611	G=0.8389
1000Genomes_30x	South Asian	Sub	1202	T=0.1448	G=0.8552
1000Genomes_30x	East Asian	Sub	1170	T=0.4641	G=0.5359
1000Genomes_30x	American	Sub	980	T=0.177	G=0.823
1000Genomes	Global	Study-wide	5008	T=0.1829	G=0.8171
1000Genomes	African	Sub	1322	T=0.0265	G=0.9735
1000Genomes	East Asian	Sub	1008	T=0.4643	G=0.5357
1000Genomes	Europe	Sub	1006	T=0.1541	G=0.8459
1000Genomes	South Asian	Sub	978	T=0.137	G=0.863
1000Genomes	American	Sub	694	T=0.179	G=0.821
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.1319	G=0.8681
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.1733	G=0.8267
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.1564	G=0.8436
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.4321	A=0.0000, G=0.5679
Korean Genome Project	KOREAN	Study-wide	1832	T=0.4279	G=0.5721
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.166	G=0.834
Northern Sweden	ACPOP	Study-wide	600	T=0.115	G=0.885
SGDP_PRJ	Global	Study-wide	496	T=0.169	G=0.831
Qatari	Global	Study-wide	216	T=0.162	G=0.838
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.532	G=0.468
Siberian	Global	Study-wide	54	T=0.24	G=0.76
The Danish reference pan genome	Danish	Study-wide	40	T=0.15	G=0.85

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 1	NC_000001.11:g.116685595T>A
GRCh38.p14 chr 1	NC_000001.11:g.116685595T>G
GRCh37.p13 chr 1	NC_000001.10:g.117228217T>A
GRCh37.p13 chr 1	NC_000001.10:g.117228217T>G

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=	A	G
GRCh38.p14 chr 1	NC_000001.11:g.116685595=	NC_000001.11:g.116685595T>A	NC_000001.11:g.116685595T>G
GRCh37.p13 chr 1	NC_000001.10:g.117228217=	NC_000001.10:g.117228217T>A	NC_000001.10:g.117228217T>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#.

78 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss640416	Aug 11, 2000 (83)
2	KWOK	ss879608	Oct 04, 2000 (86)
3	KWOK	ss995578	Oct 04, 2000 (86)
4	KWOK	ss1647562	Oct 18, 2000 (87)
5	BCM_SSAHASNP	ss9808518	Jul 11, 2003 (116)
6	WI_SSAHASNP	ss11341622	Jul 11, 2003 (116)
7	CSHL-HAPMAP	ss16434966	Feb 27, 2004 (120)
8	SSAHASNP	ss20536600	Apr 05, 2004 (121)
9	HGSV	ss84151602	Dec 15, 2007 (130)
10	BCMHGSC_JDW	ss87738780	Mar 23, 2008 (129)
11	HUMANGENOME_JCVI	ss97970206	Feb 05, 2009 (130)
12	BGI	ss106597602	Feb 05, 2009 (130)
13	ILLUMINA-UK	ss118994205	Dec 01, 2009 (131)
14	ENSEMBL	ss138066206	Dec 01, 2009 (131)
15	ENSEMBL	ss139266168	Dec 01, 2009 (131)
16	GMI	ss155579491	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss163965310	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss165094108	Jul 04, 2010 (132)
19	COMPLETE_GENOMICS	ss167040295	Jul 04, 2010 (132)
20	BUSHMAN	ss198977343	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss205432090	Jul 04, 2010 (132)
22	BL	ss253411179	May 09, 2011 (134)
23	GMI	ss275992150	May 04, 2012 (137)
24	GMI	ss284127735	Apr 25, 2013 (138)
25	PJP	ss290606079	May 09, 2011 (134)
26	1000GENOMES	ss328880743	May 09, 2011 (134)
27	TISHKOFF	ss554620052	Apr 25, 2013 (138)
28	SSMP	ss648336984	Apr 25, 2013 (138)
29	EVA-GONL	ss975609270	Aug 21, 2014 (142)
30	JMKIDD_LAB	ss1068220840	Aug 21, 2014 (142)
31	1000GENOMES	ss1292580464	Aug 21, 2014 (142)
32	DDI	ss1425948096	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1574346934	Apr 01, 2015 (144)
34	EVA_DECODE	ss1584991373	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1601070837	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1644064870	Apr 01, 2015 (144)
37	HAMMER_LAB	ss1794985820	Sep 08, 2015 (146)
38	WEILL_CORNELL_DGM	ss1918807767	Feb 12, 2016 (147)
39	GENOMED	ss1966850007	Jul 19, 2016 (147)
40	JJLAB	ss2019929480	Sep 14, 2016 (149)
41	USC_VALOUEV	ss2147948292	Dec 20, 2016 (150)
42	HUMAN_LONGEVITY	ss2166019730	Dec 20, 2016 (150)
43	SYSTEMSBIOZJU	ss2624473807	Nov 08, 2017 (151)
44	GRF	ss2697879069	Nov 08, 2017 (151)
45	GNOMAD	ss2759983820	Nov 08, 2017 (151)
46	SWEGEN	ss2987498587	Nov 08, 2017 (151)
47	SWEGEN	ss2987498588	Nov 08, 2017 (151)
48	CSHL	ss3343652326	Nov 08, 2017 (151)
49	BIOINF_KMB_FNS_UNIBA	ss3645067984	Oct 11, 2018 (152)
50	URBANLAB	ss3646760288	Oct 11, 2018 (152)
51	EGCUT_WGS	ss3655589238	Jul 12, 2019 (153)
52	EVA_DECODE	ss3687603581	Jul 12, 2019 (153)
53	ACPOP	ss3727420792	Jul 12, 2019 (153)
54	EVA	ss3746717925	Jul 12, 2019 (153)
55	PACBIO	ss3783529841	Jul 12, 2019 (153)
56	PACBIO	ss3789169977	Jul 12, 2019 (153)
57	PACBIO	ss3794042937	Jul 12, 2019 (153)
58	KHV_HUMAN_GENOMES	ss3799719066	Jul 12, 2019 (153)
59	EVA	ss3826389180	Apr 25, 2020 (154)
60	EVA	ss3836585728	Apr 25, 2020 (154)
61	EVA	ss3841994266	Apr 25, 2020 (154)
62	SGDP_PRJ	ss3849724881	Apr 25, 2020 (154)
63	KRGDB	ss3894828879	Apr 25, 2020 (154)
64	KOGIC	ss3945320576	Apr 25, 2020 (154)
65	TOPMED	ss4464933018	Apr 25, 2021 (155)
66	TOMMO_GENOMICS	ss5145846629	Apr 25, 2021 (155)
67	1000G_HIGH_COVERAGE	ss5243736262	Oct 12, 2022 (156)
68	EVA	ss5321420563	Oct 12, 2022 (156)
69	HUGCELL_USP	ss5444647970	Oct 12, 2022 (156)
70	1000G_HIGH_COVERAGE	ss5516796398	Oct 12, 2022 (156)
71	SANFORD_IMAGENETICS	ss5626370696	Oct 12, 2022 (156)
72	TOMMO_GENOMICS	ss5671164263	Oct 12, 2022 (156)
73	YY_MCH	ss5800962416	Oct 12, 2022 (156)
74	EVA	ss5832533904	Oct 12, 2022 (156)
75	EVA	ss5849082210	Oct 12, 2022 (156)
76	EVA	ss5909949028	Oct 12, 2022 (156)
77	EVA	ss5938240962	Oct 12, 2022 (156)
78	EVA	ss5979980625	Oct 12, 2022 (156)
79	1000Genomes	NC_000001.10 - 117228217	Oct 11, 2018 (152)
80	1000Genomes_30x	NC_000001.11 - 116685595	Oct 12, 2022 (156)
81	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 117228217	Oct 11, 2018 (152)
82	Genetic variation in the Estonian population	NC_000001.10 - 117228217	Oct 11, 2018 (152)
83	The Danish reference pan genome	NC_000001.10 - 117228217	Apr 25, 2020 (154)
84	gnomAD - Genomes Submission ignored due to conflicting rows: Row 23775863 (NC_000001.11:116685594:T:A 4/140124) Row 23775864 (NC_000001.11:116685594:T:G 121127/140108)	-	Apr 25, 2021 (155)
85	gnomAD - Genomes Submission ignored due to conflicting rows: Row 23775863 (NC_000001.11:116685594:T:A 4/140124) Row 23775864 (NC_000001.11:116685594:T:G 121127/140108)	-	Apr 25, 2021 (155)
86	Genome of the Netherlands Release 5	NC_000001.10 - 117228217	Apr 25, 2020 (154)
87	KOREAN population from KRGDB	NC_000001.10 - 117228217	Apr 25, 2020 (154)
88	Korean Genome Project	NC_000001.11 - 116685595	Apr 25, 2020 (154)
89	Northern Sweden	NC_000001.10 - 117228217	Jul 12, 2019 (153)
90	Qatari	NC_000001.10 - 117228217	Apr 25, 2020 (154)
91	SGDP_PRJ	NC_000001.10 - 117228217	Apr 25, 2020 (154)
92	Siberian	NC_000001.10 - 117228217	Apr 25, 2020 (154)
93	8.3KJPN	NC_000001.10 - 117228217	Apr 25, 2021 (155)
94	14KJPN	NC_000001.11 - 116685595	Oct 12, 2022 (156)
95	TopMed	NC_000001.11 - 116685595	Apr 25, 2021 (155)
96	UK 10K study - Twins	NC_000001.10 - 117228217	Oct 11, 2018 (152)
97	A Vietnamese Genetic Variation Database	NC_000001.10 - 117228217	Jul 12, 2019 (153)
98	ALFA	NC_000001.11 - 116685595	Apr 25, 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)
rs58728390	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
2006273, ss2759983820, ss2987498588, ss3894828879	NC_000001.10:117228216:T:A	NC_000001.11:116685594:T:A	(self)
939811429, ss2166019730	NC_000001.11:116685594:T:A	NC_000001.11:116685594:T:A	(self)
ss84151602	NC_000001.8:116940258:T:G	NC_000001.11:116685594:T:G	(self)
ss87738780, ss118994205, ss163965310, ss165094108, ss167040295, ss198977343, ss205432090, ss253411179, ss275992150, ss284127735, ss290606079, ss1584991373	NC_000001.9:117029739:T:G	NC_000001.11:116685594:T:G	(self)
3361514, 1862333, 1327486, 1679680, 809605, 2006273, 705657, 849697, 1741861, 464646, 3815936, 1862333, 402407, ss328880743, ss554620052, ss648336984, ss975609270, ss1068220840, ss1292580464, ss1425948096, ss1574346934, ss1601070837, ss1644064870, ss1794985820, ss1918807767, ss1966850007, ss2019929480, ss2147948292, ss2624473807, ss2697879069, ss2759983820, ss2987498587, ss3343652326, ss3655589238, ss3727420792, ss3746717925, ss3783529841, ss3789169977, ss3794042937, ss3826389180, ss3836585728, ss3849724881, ss3894828879, ss5145846629, ss5321420563, ss5626370696, ss5832533904, ss5938240962, ss5979980625	NC_000001.10:117228216:T:G	NC_000001.11:116685594:T:G	(self)
4322333, 1698577, 5001367, 28539353, 939811429, ss2166019730, ss3645067984, ss3646760288, ss3687603581, ss3799719066, ss3841994266, ss3945320576, ss4464933018, ss5243736262, ss5444647970, ss5516796398, ss5671164263, ss5800962416, ss5849082210, ss5909949028	NC_000001.11:116685594:T:G	NC_000001.11:116685594:T:G	(self)
ss9808518, ss11341622	NT_004754.14:1143801:T:G	NC_000001.11:116685594:T:G	(self)
ss16434966, ss20536600	NT_004754.15:1143801:T:G	NC_000001.11:116685594:T:G	(self)
ss640416, ss879608, ss995578, ss1647562, ss97970206, ss106597602, ss138066206, ss139266168, ss155579491	NT_032977.9:87200134:T:G	NC_000001.11:116685594:T:G	(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 rs471074

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

rs471074