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dbSNP Short Genetic Variations

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.

rs460053

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:34971285 (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=0.320919 (84944/264690, TOPMED)
G=0.316184 (44274/140026, GnomAD)
G=0.32739 (11697/35728, ALFA) (+ 18 more)
G=0.40399 (11416/28258, 14KJPN)
G=0.40179 (6734/16760, 8.3KJPN)
G=0.3282 (2102/6404, 1000G_30x)
G=0.3305 (1655/5008, 1000G)
G=0.3190 (1429/4480, Estonian)
G=0.3467 (1336/3854, ALSPAC)
G=0.3579 (1327/3708, TWINSUK)
G=0.3710 (1087/2930, KOREAN)
G=0.3173 (599/1888, HapMap)
G=0.3724 (423/1136, Daghestan)
G=0.384 (383/998, GoNL)
G=0.335 (210/626, Chileans)
G=0.350 (210/600, NorthernSweden)
A=0.338 (113/334, SGDP_PRJ)
G=0.329 (71/216, Qatari)
G=0.349 (74/212, Vietnamese)
G=0.47 (19/40, GENOME_DK)
A=0.37 (11/30, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
1 citation
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 35728 A=0.67261 G=0.32739
European Sub 25954 A=0.66206 G=0.33794
African Sub 3820 A=0.7283 G=0.2717
African Others Sub 136 A=0.750 G=0.250
African American Sub 3684 A=0.7275 G=0.2725
Asian Sub 176 A=0.625 G=0.375
East Asian Sub 116 A=0.612 G=0.388
Other Asian Sub 60 A=0.65 G=0.35
Latin American 1 Sub 310 A=0.671 G=0.329
Latin American 2 Sub 2844 A=0.6888 G=0.3112
South Asian Sub 128 A=0.555 G=0.445
Other Sub 2496 A=0.6883 G=0.3117


Help

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 A=0.679081 G=0.320919
gnomAD - Genomes Global Study-wide 140026 A=0.683816 G=0.316184
gnomAD - Genomes European Sub 75826 A=0.66228 G=0.33772
gnomAD - Genomes African Sub 41946 A=0.73063 G=0.26937
gnomAD - Genomes American Sub 13652 A=0.66994 G=0.33006
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.7028 G=0.2972
gnomAD - Genomes East Asian Sub 3128 A=0.6298 G=0.3702
gnomAD - Genomes Other Sub 2150 A=0.6674 G=0.3326
Allele Frequency Aggregator Total Global 35728 A=0.67261 G=0.32739
Allele Frequency Aggregator European Sub 25954 A=0.66206 G=0.33794
Allele Frequency Aggregator African Sub 3820 A=0.7283 G=0.2717
Allele Frequency Aggregator Latin American 2 Sub 2844 A=0.6888 G=0.3112
Allele Frequency Aggregator Other Sub 2496 A=0.6883 G=0.3117
Allele Frequency Aggregator Latin American 1 Sub 310 A=0.671 G=0.329
Allele Frequency Aggregator Asian Sub 176 A=0.625 G=0.375
Allele Frequency Aggregator South Asian Sub 128 A=0.555 G=0.445
14KJPN JAPANESE Study-wide 28258 A=0.59601 G=0.40399
8.3KJPN JAPANESE Study-wide 16760 A=0.59821 G=0.40179
1000Genomes_30x Global Study-wide 6404 A=0.6718 G=0.3282
1000Genomes_30x African Sub 1786 A=0.7368 G=0.2632
1000Genomes_30x Europe Sub 1266 A=0.6659 G=0.3341
1000Genomes_30x South Asian Sub 1202 A=0.6115 G=0.3885
1000Genomes_30x East Asian Sub 1170 A=0.6402 G=0.3598
1000Genomes_30x American Sub 980 A=0.672 G=0.328
1000Genomes Global Study-wide 5008 A=0.6695 G=0.3305
1000Genomes African Sub 1322 A=0.7413 G=0.2587
1000Genomes East Asian Sub 1008 A=0.6369 G=0.3631
1000Genomes Europe Sub 1006 A=0.6809 G=0.3191
1000Genomes South Asian Sub 978 A=0.598 G=0.402
1000Genomes American Sub 694 A=0.664 G=0.336
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.6810 G=0.3190
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.6533 G=0.3467
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.6421 G=0.3579
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.6290 G=0.3710, T=0.0000
HapMap Global Study-wide 1888 A=0.6827 G=0.3173
HapMap American Sub 770 A=0.636 G=0.364
HapMap African Sub 688 A=0.741 G=0.259
HapMap Asian Sub 254 A=0.626 G=0.374
HapMap Europe Sub 176 A=0.739 G=0.261
Genome-wide autozygosity in Daghestan Global Study-wide 1136 A=0.6276 G=0.3724
Genome-wide autozygosity in Daghestan Daghestan Sub 628 A=0.597 G=0.403
Genome-wide autozygosity in Daghestan Near_East Sub 144 A=0.722 G=0.278
Genome-wide autozygosity in Daghestan Central Asia Sub 122 A=0.566 G=0.434
Genome-wide autozygosity in Daghestan Europe Sub 108 A=0.741 G=0.259
Genome-wide autozygosity in Daghestan South Asian Sub 98 A=0.60 G=0.40
Genome-wide autozygosity in Daghestan Caucasus Sub 36 A=0.72 G=0.28
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.616 G=0.384
Chileans Chilean Study-wide 626 A=0.665 G=0.335
Northern Sweden ACPOP Study-wide 600 A=0.650 G=0.350
SGDP_PRJ Global Study-wide 334 A=0.338 G=0.662
Qatari Global Study-wide 216 A=0.671 G=0.329
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.651 G=0.349
The Danish reference pan genome Danish Study-wide 40 A=0.53 G=0.47
Siberian Global Study-wide 30 A=0.37 G=0.63
Help

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 5 NC_000005.10:g.34971285A>G
GRCh38.p14 chr 5 NC_000005.10:g.34971285A>T
GRCh37.p13 chr 5 NC_000005.9:g.34971390A>G
GRCh37.p13 chr 5 NC_000005.9:g.34971390A>T
Help

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
Help

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 5 NC_000005.10:g.34971285= NC_000005.10:g.34971285A>G NC_000005.10:g.34971285A>T
GRCh37.p13 chr 5 NC_000005.9:g.34971390= NC_000005.9:g.34971390A>G NC_000005.9:g.34971390A>T
Help

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, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss621320 Jul 16, 2000 (80)
2 CSHL-HAPMAP ss17835098 Feb 27, 2004 (120)
3 PERLEGEN ss24425342 Sep 20, 2004 (123)
4 ABI ss44586598 Mar 15, 2006 (126)
5 PERLEGEN ss68932120 May 17, 2007 (127)
6 AFFY ss76550605 Dec 08, 2007 (130)
7 HGSV ss79947502 Dec 15, 2007 (130)
8 HUMANGENOME_JCVI ss98712952 Feb 06, 2009 (130)
9 KRIBB_YJKIM ss104818123 Feb 06, 2009 (130)
10 1000GENOMES ss108953388 Jan 23, 2009 (130)
11 1000GENOMES ss111683695 Jan 25, 2009 (130)
12 ILLUMINA-UK ss116564457 Feb 14, 2009 (130)
13 GMI ss155292611 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss162167206 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss164685955 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss166408976 Jul 04, 2010 (132)
17 BUSHMAN ss200105341 Jul 04, 2010 (132)
18 1000GENOMES ss221619464 Jul 14, 2010 (132)
19 1000GENOMES ss232901335 Jul 14, 2010 (132)
20 1000GENOMES ss240084394 Jul 15, 2010 (132)
21 BL ss253367907 May 09, 2011 (134)
22 GMI ss278242740 May 04, 2012 (137)
23 GMI ss285155331 Apr 25, 2013 (138)
24 PJP ss293566609 May 09, 2011 (134)
25 ILLUMINA ss479481839 May 04, 2012 (137)
26 ILLUMINA ss485031264 May 04, 2012 (137)
27 ILLUMINA ss533025332 Sep 08, 2015 (146)
28 TISHKOFF ss558318994 Apr 25, 2013 (138)
29 SSMP ss652174090 Apr 25, 2013 (138)
30 ILLUMINA ss779594790 Sep 08, 2015 (146)
31 ILLUMINA ss780992297 Sep 08, 2015 (146)
32 ILLUMINA ss835066670 Sep 08, 2015 (146)
33 EVA-GONL ss981437867 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1072535525 Aug 21, 2014 (142)
35 1000GENOMES ss1314610166 Aug 21, 2014 (142)
36 HAMMER_LAB ss1397409994 Sep 08, 2015 (146)
37 DDI ss1430305887 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1581090106 Apr 01, 2015 (144)
39 EVA_DECODE ss1590960096 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1612638283 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1655632316 Apr 01, 2015 (144)
42 EVA_SVP ss1712756418 Apr 01, 2015 (144)
43 HAMMER_LAB ss1803348436 Sep 08, 2015 (146)
44 WEILL_CORNELL_DGM ss1924700803 Feb 12, 2016 (147)
45 GENOMED ss1970061653 Jul 19, 2016 (147)
46 JJLAB ss2022953072 Sep 14, 2016 (149)
47 USC_VALOUEV ss2151103741 Dec 20, 2016 (150)
48 HUMAN_LONGEVITY ss2272800408 Dec 20, 2016 (150)
49 SYSTEMSBIOZJU ss2625976916 Nov 08, 2017 (151)
50 GRF ss2706639936 Nov 08, 2017 (151)
51 GNOMAD ss2823168393 Nov 08, 2017 (151)
52 SWEGEN ss2996726737 Nov 08, 2017 (151)
53 BIOINF_KMB_FNS_UNIBA ss3025261877 Nov 08, 2017 (151)
54 CSHL ss3346331951 Nov 08, 2017 (151)
55 ILLUMINA ss3629212815 Oct 12, 2018 (152)
56 ILLUMINA ss3632194575 Oct 12, 2018 (152)
57 ILLUMINA ss3642408800 Oct 12, 2018 (152)
58 URBANLAB ss3648031058 Oct 12, 2018 (152)
59 EGCUT_WGS ss3664619393 Jul 13, 2019 (153)
60 EVA_DECODE ss3714454169 Jul 13, 2019 (153)
61 ACPOP ss3732251198 Jul 13, 2019 (153)
62 EVA ss3763284785 Jul 13, 2019 (153)
63 KHV_HUMAN_GENOMES ss3806460531 Jul 13, 2019 (153)
64 EVA ss3829188931 Apr 26, 2020 (154)
65 EVA ss3838063717 Apr 26, 2020 (154)
66 EVA ss3843502953 Apr 26, 2020 (154)
67 SGDP_PRJ ss3861599364 Apr 26, 2020 (154)
68 KRGDB ss3908071068 Apr 26, 2020 (154)
69 TOPMED ss4655662043 Apr 26, 2021 (155)
70 TOMMO_GENOMICS ss5171183577 Apr 26, 2021 (155)
71 1000G_HIGH_COVERAGE ss5263510778 Oct 13, 2022 (156)
72 EVA ss5315044772 Oct 13, 2022 (156)
73 EVA ss5356787676 Oct 13, 2022 (156)
74 HUGCELL_USP ss5461783629 Oct 13, 2022 (156)
75 EVA ss5507977085 Oct 13, 2022 (156)
76 1000G_HIGH_COVERAGE ss5546904505 Oct 13, 2022 (156)
77 SANFORD_IMAGENETICS ss5637558608 Oct 13, 2022 (156)
78 TOMMO_GENOMICS ss5707075775 Oct 13, 2022 (156)
79 YY_MCH ss5806180768 Oct 13, 2022 (156)
80 EVA ss5834767810 Oct 13, 2022 (156)
81 EVA ss5854764876 Oct 13, 2022 (156)
82 EVA ss5893698439 Oct 13, 2022 (156)
83 EVA ss5965973547 Oct 13, 2022 (156)
84 1000Genomes NC_000005.9 - 34971390 Oct 12, 2018 (152)
85 1000Genomes_30x NC_000005.10 - 34971285 Oct 13, 2022 (156)
86 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 34971390 Oct 12, 2018 (152)
87 Chileans NC_000005.9 - 34971390 Apr 26, 2020 (154)
88 Genome-wide autozygosity in Daghestan NC_000005.8 - 35007147 Apr 26, 2020 (154)
89 Genetic variation in the Estonian population NC_000005.9 - 34971390 Oct 12, 2018 (152)
90 The Danish reference pan genome NC_000005.9 - 34971390 Apr 26, 2020 (154)
91 gnomAD - Genomes NC_000005.10 - 34971285 Apr 26, 2021 (155)
92 Genome of the Netherlands Release 5 NC_000005.9 - 34971390 Apr 26, 2020 (154)
93 HapMap NC_000005.10 - 34971285 Apr 26, 2020 (154)
94 KOREAN population from KRGDB NC_000005.9 - 34971390 Apr 26, 2020 (154)
95 Northern Sweden NC_000005.9 - 34971390 Jul 13, 2019 (153)
96 Qatari NC_000005.9 - 34971390 Apr 26, 2020 (154)
97 SGDP_PRJ NC_000005.9 - 34971390 Apr 26, 2020 (154)
98 Siberian NC_000005.9 - 34971390 Apr 26, 2020 (154)
99 8.3KJPN NC_000005.9 - 34971390 Apr 26, 2021 (155)
100 14KJPN NC_000005.10 - 34971285 Oct 13, 2022 (156)
101 TopMed NC_000005.10 - 34971285 Apr 26, 2021 (155)
102 UK 10K study - Twins NC_000005.9 - 34971390 Oct 12, 2018 (152)
103 A Vietnamese Genetic Variation Database NC_000005.9 - 34971390 Jul 13, 2019 (153)
104 ALFA NC_000005.10 - 34971285 Apr 26, 2021 (155)
Help

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)
rs17304668 Oct 08, 2004 (123)
rs56589977 May 25, 2008 (130)
rs60067941 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
385071, ss76550605, ss79947502, ss108953388, ss111683695, ss116564457, ss162167206, ss164685955, ss166408976, ss200105341, ss253367907, ss278242740, ss285155331, ss293566609, ss485031264, ss1397409994, ss1590960096, ss1712756418 NC_000005.8:35007146:A:G NC_000005.10:34971284:A:G (self)
26193429, 14567108, 343348, 10357641, 7255045, 6473904, 15248462, 5536063, 6742733, 13616344, 3620095, 29152884, 14567108, 3238501, ss221619464, ss232901335, ss240084394, ss479481839, ss533025332, ss558318994, ss652174090, ss779594790, ss780992297, ss835066670, ss981437867, ss1072535525, ss1314610166, ss1430305887, ss1581090106, ss1612638283, ss1655632316, ss1803348436, ss1924700803, ss1970061653, ss2022953072, ss2151103741, ss2625976916, ss2706639936, ss2823168393, ss2996726737, ss3346331951, ss3629212815, ss3632194575, ss3642408800, ss3664619393, ss3732251198, ss3763284785, ss3829188931, ss3838063717, ss3861599364, ss3908071068, ss5171183577, ss5315044772, ss5356787676, ss5507977085, ss5637558608, ss5834767810, ss5965973547 NC_000005.9:34971389:A:G NC_000005.10:34971284:A:G (self)
34430440, 185052445, 2844148, 40912879, 493039600, 11477673949, ss2272800408, ss3025261877, ss3648031058, ss3714454169, ss3806460531, ss3843502953, ss4655662043, ss5263510778, ss5461783629, ss5546904505, ss5707075775, ss5806180768, ss5854764876, ss5893698439 NC_000005.10:34971284:A:G NC_000005.10:34971284:A:G (self)
ss17835098 NT_006576.14:17423495:A:G NC_000005.10:34971284:A:G (self)
ss621320, ss24425342, ss44586598, ss68932120, ss98712952, ss104818123, ss155292611 NT_006576.16:34961389:A:G NC_000005.10:34971284:A:G (self)
15248462, ss3908071068 NC_000005.9:34971389:A:T NC_000005.10:34971284:A:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs460053
PMID Title Author Year Journal
16400611 Genomewide linkage scan of 409 European-ancestry and African American families with schizophrenia: suggestive evidence of linkage at 8p23.3-p21.2 and 11p13.1-q14.1 in the combined sample. Suarez BK et al. 2006 American journal of human genetics
Help

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.

Software version is: 2.0.1.post761+d5e8e07