Name: rs471057
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.

rs471057

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:164222707 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.224376 (59390/264690, TOPMED)
G=0.231641 (32143/138762, GnomAD)
G=0.09562 (2702/28258, 14KJPN) (+ 14 more)
G=0.23965 (4527/18890, ALFA)
G=0.09749 (1634/16760, 8.3KJPN)
G=0.2127 (1362/6404, 1000G_30x)
G=0.2161 (1082/5008, 1000G)
G=0.2475 (954/3854, ALSPAC)
G=0.2497 (926/3708, TWINSUK)
G=0.1184 (347/2930, KOREAN)
G=0.254 (253/998, GoNL)
G=0.248 (149/600, NorthernSweden)
A=0.399 (87/218, SGDP_PRJ)
G=0.162 (35/216, Qatari)
G=0.238 (50/210, Vietnamese)
G=0.17 (7/40, GENOME_DK)
A=0.46 (12/26, 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	18890	A=0.76035	G=0.23965
European	Sub	14286	A=0.74920	G=0.25080
African	Sub	2946	A=0.8245	G=0.1755
African Others	Sub	114	A=0.763	G=0.237
African American	Sub	2832	A=0.8270	G=0.1730
Asian	Sub	112	A=0.875	G=0.125
East Asian	Sub	86	A=0.87	G=0.13
Other Asian	Sub	26	A=0.88	G=0.12
Latin American 1	Sub	146	A=0.712	G=0.288
Latin American 2	Sub	610	A=0.703	G=0.297
South Asian	Sub	98	A=0.68	G=0.32
Other	Sub	692	A=0.770	G=0.230

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=0.775624	G=0.224376
gnomAD - Genomes	Global	Study-wide	138762	A=0.768359	G=0.231641
gnomAD - Genomes	European	Sub	74870	A=0.73992	G=0.26008
gnomAD - Genomes	African	Sub	41894	A=0.82742	G=0.17258
gnomAD - Genomes	American	Sub	13466	A=0.73162	G=0.26838
gnomAD - Genomes	Ashkenazi Jewish	Sub	3296	A=0.7096	G=0.2904
gnomAD - Genomes	East Asian	Sub	3118	A=0.8765	G=0.1235
gnomAD - Genomes	Other	Sub	2118	A=0.7710	G=0.2290
14KJPN	JAPANESE	Study-wide	28258	A=0.90438	G=0.09562
Allele Frequency Aggregator	Total	Global	18890	A=0.76035	G=0.23965
Allele Frequency Aggregator	European	Sub	14286	A=0.74920	G=0.25080
Allele Frequency Aggregator	African	Sub	2946	A=0.8245	G=0.1755
Allele Frequency Aggregator	Other	Sub	692	A=0.770	G=0.230
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.703	G=0.297
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.712	G=0.288
Allele Frequency Aggregator	Asian	Sub	112	A=0.875	G=0.125
Allele Frequency Aggregator	South Asian	Sub	98	A=0.68	G=0.32
8.3KJPN	JAPANESE	Study-wide	16760	A=0.90251	G=0.09749
1000Genomes_30x	Global	Study-wide	6404	A=0.7873	G=0.2127
1000Genomes_30x	African	Sub	1786	A=0.8432	G=0.1568
1000Genomes_30x	Europe	Sub	1266	A=0.7488	G=0.2512
1000Genomes_30x	South Asian	Sub	1202	A=0.7388	G=0.2612
1000Genomes_30x	East Asian	Sub	1170	A=0.8564	G=0.1436
1000Genomes_30x	American	Sub	980	A=0.712	G=0.288
1000Genomes	Global	Study-wide	5008	A=0.7839	G=0.2161
1000Genomes	African	Sub	1322	A=0.8374	G=0.1626
1000Genomes	East Asian	Sub	1008	A=0.8581	G=0.1419
1000Genomes	Europe	Sub	1006	A=0.7366	G=0.2634
1000Genomes	South Asian	Sub	978	A=0.738	G=0.262
1000Genomes	American	Sub	694	A=0.707	G=0.293
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.7525	G=0.2475
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.7503	G=0.2497
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.8816	G=0.1184
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.746	G=0.254
Northern Sweden	ACPOP	Study-wide	600	A=0.752	G=0.248
SGDP_PRJ	Global	Study-wide	218	A=0.399	G=0.601
Qatari	Global	Study-wide	216	A=0.838	G=0.162
A Vietnamese Genetic Variation Database	Global	Study-wide	210	A=0.762	G=0.238
The Danish reference pan genome	Danish	Study-wide	40	A=0.82	G=0.17
Siberian	Global	Study-wide	26	A=0.46	G=0.54

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 3	NC_000003.12:g.164222707A>G
GRCh37.p13 chr 3	NC_000003.11:g.163940495A>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	A=	G
GRCh38.p14 chr 3	NC_000003.12:g.164222707=	NC_000003.12:g.164222707A>G
GRCh37.p13 chr 3	NC_000003.11:g.163940495=	NC_000003.11:g.163940495A>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#.

59 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss640399	Aug 11, 2000 (83)
2	TSC-CSHL	ss2406531	Oct 23, 2000 (92)
3	SC_JCM	ss2493893	Nov 09, 2000 (92)
4	TSC-CSHL	ss5566871	Oct 08, 2002 (108)
5	WI_SSAHASNP	ss6707850	Feb 20, 2003 (111)
6	BCM_SSAHASNP	ss14216269	Dec 05, 2003 (119)
7	PERLEGEN	ss24312363	Sep 20, 2004 (123)
8	ABI	ss44471937	Mar 13, 2006 (126)
9	HUMANGENOME_JCVI	ss96071222	Feb 06, 2009 (130)
10	1000GENOMES	ss112654000	Jan 25, 2009 (130)
11	ENSEMBL	ss143007270	Dec 01, 2009 (131)
12	BUSHMAN	ss203466840	Jul 04, 2010 (132)
13	BCM-HGSC-SUB	ss206191738	Jul 04, 2010 (132)
14	1000GENOMES	ss220551084	Jul 14, 2010 (132)
15	1000GENOMES	ss232123329	Jul 14, 2010 (132)
16	1000GENOMES	ss239475218	Jul 15, 2010 (132)
17	GMI	ss277437939	May 04, 2012 (137)
18	PJP	ss292965689	May 09, 2011 (134)
19	SSMP	ss650826812	Apr 25, 2013 (138)
20	EVA-GONL	ss979401073	Aug 21, 2014 (142)
21	JMKIDD_LAB	ss1071013176	Aug 21, 2014 (142)
22	1000GENOMES	ss1307068108	Aug 21, 2014 (142)
23	DDI	ss1429657845	Apr 01, 2015 (144)
24	EVA_GENOME_DK	ss1580276407	Apr 01, 2015 (144)
25	EVA_UK10K_ALSPAC	ss1608696669	Apr 01, 2015 (144)
26	EVA_UK10K_TWINSUK	ss1651690702	Apr 01, 2015 (144)
27	WEILL_CORNELL_DGM	ss1922623971	Feb 12, 2016 (147)
28	JJLAB	ss2021886875	Sep 14, 2016 (149)
29	USC_VALOUEV	ss2149982680	Dec 20, 2016 (150)
30	HUMAN_LONGEVITY	ss2257726436	Dec 20, 2016 (150)
31	SYSTEMSBIOZJU	ss2625445002	Nov 08, 2017 (151)
32	GRF	ss2705401954	Nov 08, 2017 (151)
33	GNOMAD	ss2801739644	Nov 08, 2017 (151)
34	SWEGEN	ss2993561540	Nov 08, 2017 (151)
35	BIOINF_KMB_FNS_UNIBA	ss3024711876	Nov 08, 2017 (151)
36	CSHL	ss3345372787	Nov 08, 2017 (151)
37	URBANLAB	ss3647576494	Oct 12, 2018 (152)
38	EVA_DECODE	ss3710729308	Jul 13, 2019 (153)
39	ACPOP	ss3730549472	Jul 13, 2019 (153)
40	EVA	ss3760974235	Jul 13, 2019 (153)
41	KHV_HUMAN_GENOMES	ss3804108330	Jul 13, 2019 (153)
42	EVA	ss3828191591	Apr 25, 2020 (154)
43	EVA	ss3837529483	Apr 25, 2020 (154)
44	EVA	ss3842961333	Apr 25, 2020 (154)
45	SGDP_PRJ	ss3857451042	Apr 25, 2020 (154)
46	KRGDB	ss3903511978	Apr 25, 2020 (154)
47	TOPMED	ss4591571523	Apr 26, 2021 (155)
48	TOMMO_GENOMICS	ss5162609911	Apr 26, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5256820311	Oct 12, 2022 (156)
50	HUGCELL_USP	ss5455881842	Oct 12, 2022 (156)
51	EVA	ss5507291960	Oct 12, 2022 (156)
52	1000G_HIGH_COVERAGE	ss5536679278	Oct 12, 2022 (156)
53	SANFORD_IMAGENETICS	ss5633644798	Oct 12, 2022 (156)
54	TOMMO_GENOMICS	ss5695782435	Oct 12, 2022 (156)
55	YY_MCH	ss5804447271	Oct 12, 2022 (156)
56	EVA	ss5826787826	Oct 12, 2022 (156)
57	EVA	ss5853937615	Oct 12, 2022 (156)
58	EVA	ss5871916350	Oct 12, 2022 (156)
59	EVA	ss5962015554	Oct 12, 2022 (156)
60	1000Genomes	NC_000003.11 - 163940495	Oct 12, 2018 (152)
61	1000Genomes_30x	NC_000003.12 - 164222707	Oct 12, 2022 (156)
62	The Avon Longitudinal Study of Parents and Children	NC_000003.11 - 163940495	Oct 12, 2018 (152)
63	The Danish reference pan genome	NC_000003.11 - 163940495	Apr 25, 2020 (154)
64	gnomAD - Genomes	NC_000003.12 - 164222707	Apr 26, 2021 (155)
65	Genome of the Netherlands Release 5	NC_000003.11 - 163940495	Apr 25, 2020 (154)
66	KOREAN population from KRGDB	NC_000003.11 - 163940495	Apr 25, 2020 (154)
67	Northern Sweden	NC_000003.11 - 163940495	Jul 13, 2019 (153)
68	Qatari	NC_000003.11 - 163940495	Apr 25, 2020 (154)
69	SGDP_PRJ	NC_000003.11 - 163940495	Apr 25, 2020 (154)
70	Siberian	NC_000003.11 - 163940495	Apr 25, 2020 (154)
71	8.3KJPN	NC_000003.11 - 163940495	Apr 26, 2021 (155)
72	14KJPN	NC_000003.12 - 164222707	Oct 12, 2022 (156)
73	TopMed	NC_000003.12 - 164222707	Apr 26, 2021 (155)
74	UK 10K study - Twins	NC_000003.11 - 163940495	Oct 12, 2018 (152)
75	A Vietnamese Genetic Variation Database	NC_000003.11 - 163940495	Jul 13, 2019 (153)
76	ALFA	NC_000003.12 - 164222707	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)
rs1562744	Jan 18, 2001 (92)
rs1667791	Jan 18, 2001 (92)
rs17813514	Oct 07, 2004 (123)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss112654000, ss203466840, ss206191738, ss277437939, ss292965689	NC_000003.10:165423188:A:G	NC_000003.12:164222706:A:G	(self)
18366114, 10233172, 6441346, 4496843, 10689372, 3834337, 4665901, 9468022, 2499034, 20579218, 10233172, 2237207, ss220551084, ss232123329, ss239475218, ss650826812, ss979401073, ss1071013176, ss1307068108, ss1429657845, ss1580276407, ss1608696669, ss1651690702, ss1922623971, ss2021886875, ss2149982680, ss2625445002, ss2705401954, ss2801739644, ss2993561540, ss3345372787, ss3730549472, ss3760974235, ss3828191591, ss3837529483, ss3857451042, ss3903511978, ss5162609911, ss5507291960, ss5633644798, ss5826787826, ss5962015554	NC_000003.11:163940494:A:G	NC_000003.12:164222706:A:G	(self)
24205213, 130457055, 29619539, 428949078, 1616685776, ss2257726436, ss3024711876, ss3647576494, ss3710729308, ss3804108330, ss3842961333, ss4591571523, ss5256820311, ss5455881842, ss5536679278, ss5695782435, ss5804447271, ss5853937615, ss5871916350	NC_000003.12:164222706:A:G	NC_000003.12:164222706:A:G	(self)
ss14216269	NT_005612.14:70435652:A:G	NC_000003.12:164222706:A:G	(self)
ss640399, ss2406531, ss2493893, ss5566871, ss6707850, ss24312363, ss44471937, ss96071222, ss143007270	NT_005612.16:70435640:A:G	NC_000003.12:164222706:A: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 rs471057

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

rs471057