Name: rs852962
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.

rs852962

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:71477911 (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 / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.420586 (111325/264690, TOPMED)
G=0.420972 (58883/139874, GnomAD)
G=0.24733 (6989/28258, 14KJPN) (+ 18 more)
G=0.41507 (9862/23760, ALFA)
G=0.24791 (4155/16760, 8.3KJPN)
G=0.3668 (2349/6404, 1000G_30x)
G=0.3564 (1785/5008, 1000G)
G=0.3525 (1579/4480, Estonian)
G=0.2235 (655/2930, KOREAN)
G=0.3420 (710/2076, HGDP_Stanford)
G=0.2102 (385/1832, Korea1K)
G=0.4297 (727/1692, HapMap)
G=0.3357 (380/1132, Daghestan)
G=0.365 (364/998, GoNL)
G=0.263 (158/600, NorthernSweden)
A=0.340 (106/312, SGDP_PRJ)
G=0.403 (87/216, Qatari)
G=0.171 (37/216, Vietnamese)
G=0.44 (40/90, Ancient Sardinia)
G=0.28 (11/40, GENOME_DK)
A=0.36 (8/22, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105377853 : 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	23760	A=0.58493	G=0.41507, T=0.00000
European	Sub	15630	A=0.63960	G=0.36040, T=0.00000
African	Sub	6270	A=0.4335	G=0.5665, T=0.0000
African Others	Sub	212	A=0.401	G=0.599, T=0.000
African American	Sub	6058	A=0.4346	G=0.5654, T=0.0000
Asian	Sub	122	A=0.803	G=0.197, T=0.000
East Asian	Sub	96	A=0.80	G=0.20, T=0.00
Other Asian	Sub	26	A=0.81	G=0.19, T=0.00
Latin American 1	Sub	158	A=0.589	G=0.411, T=0.000
Latin American 2	Sub	664	A=0.681	G=0.319, T=0.000
South Asian	Sub	100	A=0.69	G=0.31, T=0.00
Other	Sub	816	A=0.577	G=0.423, T=0.000

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=0.579414	G=0.420586
gnomAD - Genomes	Global	Study-wide	139874	A=0.579028	G=0.420972
gnomAD - Genomes	European	Sub	75794	A=0.63914	G=0.36086
gnomAD - Genomes	African	Sub	41900	A=0.42668	G=0.57332
gnomAD - Genomes	American	Sub	13596	A=0.66049	G=0.33951
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	A=0.5660	G=0.4340
gnomAD - Genomes	East Asian	Sub	3124	A=0.8163	G=0.1837
gnomAD - Genomes	Other	Sub	2142	A=0.5892	G=0.4108
14KJPN	JAPANESE	Study-wide	28258	A=0.75267	G=0.24733
Allele Frequency Aggregator	Total	Global	23760	A=0.58493	G=0.41507, T=0.00000
Allele Frequency Aggregator	European	Sub	15630	A=0.63960	G=0.36040, T=0.00000
Allele Frequency Aggregator	African	Sub	6270	A=0.4335	G=0.5665, T=0.0000
Allele Frequency Aggregator	Other	Sub	816	A=0.577	G=0.423, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	664	A=0.681	G=0.319, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	158	A=0.589	G=0.411, T=0.000
Allele Frequency Aggregator	Asian	Sub	122	A=0.803	G=0.197, T=0.000
Allele Frequency Aggregator	South Asian	Sub	100	A=0.69	G=0.31, T=0.00
8.3KJPN	JAPANESE	Study-wide	16760	A=0.75209	G=0.24791
1000Genomes_30x	Global	Study-wide	6404	A=0.6332	G=0.3668
1000Genomes_30x	African	Sub	1786	A=0.3959	G=0.6041
1000Genomes_30x	Europe	Sub	1266	A=0.6327	G=0.3673
1000Genomes_30x	South Asian	Sub	1202	A=0.7646	G=0.2354
1000Genomes_30x	East Asian	Sub	1170	A=0.8068	G=0.1932
1000Genomes_30x	American	Sub	980	A=0.698	G=0.302
1000Genomes	Global	Study-wide	5008	A=0.6436	G=0.3564
1000Genomes	African	Sub	1322	A=0.4070	G=0.5930
1000Genomes	East Asian	Sub	1008	A=0.8085	G=0.1915
1000Genomes	Europe	Sub	1006	A=0.6362	G=0.3638
1000Genomes	South Asian	Sub	978	A=0.769	G=0.231
1000Genomes	American	Sub	694	A=0.689	G=0.311
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.6475	G=0.3525
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.7765	G=0.2235
HGDP-CEPH-db Supplement 1	Global	Study-wide	2076	A=0.6580	G=0.3420
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	A=0.770	G=0.230
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	412	A=0.731	G=0.269
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	348	A=0.598	G=0.402
HGDP-CEPH-db Supplement 1	Europe	Sub	320	A=0.625	G=0.375
HGDP-CEPH-db Supplement 1	Africa	Sub	238	A=0.508	G=0.492
HGDP-CEPH-db Supplement 1	America	Sub	216	A=0.745	G=0.255
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	A=0.18	G=0.82
Korean Genome Project	KOREAN	Study-wide	1832	A=0.7898	G=0.2102
HapMap	Global	Study-wide	1692	A=0.5703	G=0.4297
HapMap	American	Sub	758	A=0.665	G=0.335
HapMap	African	Sub	686	A=0.402	G=0.598
HapMap	Asian	Sub	248	A=0.746	G=0.254
Genome-wide autozygosity in Daghestan	Global	Study-wide	1132	A=0.6643	G=0.3357
Genome-wide autozygosity in Daghestan	Daghestan	Sub	628	A=0.670	G=0.330
Genome-wide autozygosity in Daghestan	Near_East	Sub	144	A=0.542	G=0.458
Genome-wide autozygosity in Daghestan	Central Asia	Sub	120	A=0.733	G=0.267
Genome-wide autozygosity in Daghestan	Europe	Sub	108	A=0.657	G=0.343
Genome-wide autozygosity in Daghestan	South Asian	Sub	96	A=0.76	G=0.24
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	A=0.58	G=0.42
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.635	G=0.365
Northern Sweden	ACPOP	Study-wide	600	A=0.737	G=0.263
SGDP_PRJ	Global	Study-wide	312	A=0.340	G=0.660
Qatari	Global	Study-wide	216	A=0.597	G=0.403
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.829	G=0.171
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	90	A=0.56	G=0.44
The Danish reference pan genome	Danish	Study-wide	40	A=0.72	G=0.28
Siberian	Global	Study-wide	22	A=0.36	G=0.64

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 6	NC_000006.12:g.71477911A>G
GRCh38.p14 chr 6	NC_000006.12:g.71477911A>T
GRCh37.p13 chr 6	NC_000006.11:g.72187614A>G
GRCh37.p13 chr 6	NC_000006.11:g.72187614A>T

Gene: LOC105377853, uncharacterized LOC105377853 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105377853 transcript	XR_942683.3:n.	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	A=	G	T
GRCh38.p14 chr 6	NC_000006.12:g.71477911=	NC_000006.12:g.71477911A>G	NC_000006.12:g.71477911A>T
GRCh37.p13 chr 6	NC_000006.11:g.72187614=	NC_000006.11:g.72187614A>G	NC_000006.11:g.72187614A>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#.

84 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss1232198	Oct 05, 2000 (86)
2	KWOK	ss1725474	Oct 18, 2000 (87)
3	TSC-CSHL	ss2367875	Oct 23, 2000 (88)
4	SC_JCM	ss2580286	Nov 08, 2000 (89)
5	BCM_SSAHASNP	ss10303091	Jul 11, 2003 (116)
6	SC_SNP	ss13053127	Dec 05, 2003 (119)
7	CSHL-HAPMAP	ss20268671	Feb 27, 2004 (120)
8	ABI	ss42815538	Mar 14, 2006 (126)
9	ILLUMINA	ss68021939	Dec 02, 2006 (127)
10	ILLUMINA	ss71586570	May 18, 2007 (127)
11	ILLUMINA	ss75408467	Dec 07, 2007 (129)
12	BGI	ss104325712	Dec 01, 2009 (131)
13	1000GENOMES	ss110317570	Jan 24, 2009 (130)
14	1000GENOMES	ss114545193	Jan 25, 2009 (130)
15	KRIBB_YJKIM	ss119370400	Dec 01, 2009 (131)
16	GMI	ss157126138	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss162489995	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss163698216	Jul 04, 2010 (132)
19	ILLUMINA	ss174750102	Jul 04, 2010 (132)
20	BUSHMAN	ss202002941	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss207568229	Jul 04, 2010 (132)
22	1000GENOMES	ss222463828	Jul 14, 2010 (132)
23	1000GENOMES	ss233528886	Jul 15, 2010 (132)
24	1000GENOMES	ss240573194	Jul 15, 2010 (132)
25	GMI	ss278860876	May 04, 2012 (137)
26	GMI	ss285436148	Apr 25, 2013 (138)
27	PJP	ss293632958	May 09, 2011 (134)
28	ILLUMINA	ss410867274	Sep 17, 2011 (135)
29	ILLUMINA	ss537565420	Sep 08, 2015 (146)
30	TISHKOFF	ss559284021	Apr 25, 2013 (138)
31	SSMP	ss653240392	Apr 25, 2013 (138)
32	EVA-GONL	ss983078426	Aug 21, 2014 (142)
33	JMKIDD_LAB	ss1073720337	Aug 21, 2014 (142)
34	1000GENOMES	ss1320679283	Aug 21, 2014 (142)
35	HAMMER_LAB	ss1397459568	Sep 08, 2015 (146)
36	DDI	ss1430775996	Apr 01, 2015 (144)
37	EVA_GENOME_DK	ss1581732027	Apr 01, 2015 (144)
38	EVA_DECODE	ss1592620713	Apr 01, 2015 (144)
39	EVA_SVP	ss1712872003	Apr 01, 2015 (144)
40	HAMMER_LAB	ss1804496726	Sep 08, 2015 (146)
41	WEILL_CORNELL_DGM	ss1926334900	Feb 12, 2016 (147)
42	GENOMED	ss1970431046	Jul 19, 2016 (147)
43	JJLAB	ss2023809388	Sep 14, 2016 (149)
44	USC_VALOUEV	ss2152001206	Dec 20, 2016 (150)
45	HUMAN_LONGEVITY	ss2285018529	Dec 20, 2016 (150)
46	GRF	ss2707609863	Nov 08, 2017 (151)
47	GNOMAD	ss2840529185	Nov 08, 2017 (151)
48	SWEGEN	ss2999304639	Nov 08, 2017 (151)
49	BIOINF_KMB_FNS_UNIBA	ss3025697925	Nov 08, 2017 (151)
50	CSHL	ss3347042731	Nov 08, 2017 (151)
51	ILLUMINA	ss3629574446	Oct 12, 2018 (152)
52	ILLUMINA	ss3638637122	Oct 12, 2018 (152)
53	ILLUMINA	ss3643577692	Oct 12, 2018 (152)
54	URBANLAB	ss3648383759	Oct 12, 2018 (152)
55	EGCUT_WGS	ss3667173593	Jul 13, 2019 (153)
56	EVA_DECODE	ss3717486405	Jul 13, 2019 (153)
57	ACPOP	ss3733629767	Jul 13, 2019 (153)
58	EVA	ss3765184552	Jul 13, 2019 (153)
59	PACBIO	ss3785512899	Jul 13, 2019 (153)
60	PACBIO	ss3790858076	Jul 13, 2019 (153)
61	PACBIO	ss3795737133	Jul 13, 2019 (153)
62	KHV_HUMAN_GENOMES	ss3808333124	Jul 13, 2019 (153)
63	EVA	ss3829996377	Apr 26, 2020 (154)
64	EVA	ss3838478066	Apr 26, 2020 (154)
65	EVA	ss3843925111	Apr 26, 2020 (154)
66	HGDP	ss3847837991	Apr 26, 2020 (154)
67	SGDP_PRJ	ss3864869919	Apr 26, 2020 (154)
68	KRGDB	ss3911736399	Apr 26, 2020 (154)
69	KOGIC	ss3959312476	Apr 26, 2020 (154)
70	EVA	ss3985229806	Apr 26, 2021 (155)
71	TOPMED	ss4707800717	Apr 26, 2021 (155)
72	TOMMO_GENOMICS	ss5178122016	Apr 26, 2021 (155)
73	1000G_HIGH_COVERAGE	ss5268940985	Oct 17, 2022 (156)
74	EVA	ss5366484218	Oct 17, 2022 (156)
75	HUGCELL_USP	ss5466535996	Oct 17, 2022 (156)
76	EVA	ss5508552672	Oct 17, 2022 (156)
77	1000G_HIGH_COVERAGE	ss5555126015	Oct 17, 2022 (156)
78	SANFORD_IMAGENETICS	ss5640682875	Oct 17, 2022 (156)
79	TOMMO_GENOMICS	ss5716487468	Oct 17, 2022 (156)
80	YY_MCH	ss5807602315	Oct 17, 2022 (156)
81	EVA	ss5842444588	Oct 17, 2022 (156)
82	EVA	ss5855411874	Oct 17, 2022 (156)
83	EVA	ss5884353610	Oct 17, 2022 (156)
84	EVA	ss5969177343	Oct 17, 2022 (156)
85	1000Genomes	NC_000006.11 - 72187614	Oct 12, 2018 (152)
86	1000Genomes_30x	NC_000006.12 - 71477911	Oct 17, 2022 (156)
87	Genome-wide autozygosity in Daghestan	NC_000006.10 - 72244335	Apr 26, 2020 (154)
88	Genetic variation in the Estonian population	NC_000006.11 - 72187614	Oct 12, 2018 (152)
89	The Danish reference pan genome	NC_000006.11 - 72187614	Apr 26, 2020 (154)
90	gnomAD - Genomes	NC_000006.12 - 71477911	Apr 26, 2021 (155)
91	Genome of the Netherlands Release 5	NC_000006.11 - 72187614	Apr 26, 2020 (154)
92	HGDP-CEPH-db Supplement 1	NC_000006.10 - 72244335	Apr 26, 2020 (154)
93	HapMap	NC_000006.12 - 71477911	Apr 26, 2020 (154)
94	KOREAN population from KRGDB	NC_000006.11 - 72187614	Apr 26, 2020 (154)
95	Korean Genome Project	NC_000006.12 - 71477911	Apr 26, 2020 (154)
96	Northern Sweden	NC_000006.11 - 72187614	Jul 13, 2019 (153)
97	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000006.11 - 72187614	Apr 26, 2021 (155)
98	Qatari	NC_000006.11 - 72187614	Apr 26, 2020 (154)
99	SGDP_PRJ	NC_000006.11 - 72187614	Apr 26, 2020 (154)
100	Siberian	NC_000006.11 - 72187614	Apr 26, 2020 (154)
101	8.3KJPN	NC_000006.11 - 72187614	Apr 26, 2021 (155)
102	14KJPN	NC_000006.12 - 71477911	Oct 17, 2022 (156)
103	TopMed	NC_000006.12 - 71477911	Apr 26, 2021 (155)
104	A Vietnamese Genetic Variation Database	NC_000006.11 - 72187614	Jul 13, 2019 (153)
105	ALFA	NC_000006.12 - 71477911	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
434136, 515883, ss110317570, ss114545193, ss162489995, ss163698216, ss202002941, ss207568229, ss278860876, ss285436148, ss293632958, ss410867274, ss1397459568, ss1592620713, ss1712872003, ss3643577692, ss3847837991	NC_000006.10:72244334:A:G	NC_000006.12:71477910:A:G	(self)
32487402, 12911841, 7896966, 8063810, 18913793, 6914632, 455733, 8376830, 16886899, 4517560, 36091323, 4020768, ss222463828, ss233528886, ss240573194, ss537565420, ss559284021, ss653240392, ss983078426, ss1073720337, ss1320679283, ss1430775996, ss1581732027, ss1804496726, ss1926334900, ss1970431046, ss2023809388, ss2152001206, ss2707609863, ss2840529185, ss2999304639, ss3347042731, ss3629574446, ss3638637122, ss3667173593, ss3733629767, ss3765184552, ss3785512899, ss3790858076, ss3795737133, ss3829996377, ss3838478066, ss3864869919, ss3911736399, ss3985229806, ss5178122016, ss5366484218, ss5508552672, ss5640682875, ss5842444588, ss5969177343	NC_000006.11:72187613:A:G	NC_000006.12:71477910:A:G	(self)
42651950, 229293741, 3161064, 15690477, 50324572, 545178275, 1185438743, ss2285018529, ss3025697925, ss3648383759, ss3717486405, ss3808333124, ss3843925111, ss3959312476, ss4707800717, ss5268940985, ss5466535996, ss5555126015, ss5716487468, ss5807602315, ss5855411874, ss5884353610	NC_000006.12:71477910:A:G	NC_000006.12:71477910:A:G	(self)
ss10303091, ss13053127, ss20268671	NT_007299.12:10007786:A:G	NC_000006.12:71477910:A:G	(self)
ss1232198, ss1725474, ss2367875, ss2580286, ss42815538, ss68021939, ss71586570, ss75408467, ss104325712, ss119370400, ss157126138, ss174750102	NT_007299.13:10307447:A:G	NC_000006.12:71477910:A:G	(self)
1185438743	NC_000006.12:71477910:A:T	NC_000006.12:71477910:A: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 rs852962

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

rs852962