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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.

rs3888820

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:20266382 (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>C / A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.275662 (72965/264690, TOPMED)
A=0.273716 (38346/140094, GnomAD)
A=0.31923 (12019/37650, ALFA) (+ 17 more)
A=0.12704 (3590/28258, 14KJPN)
A=0.13013 (2181/16760, 8.3KJPN)
A=0.2032 (1301/6404, 1000G_30x)
A=0.2013 (1008/5008, 1000G)
A=0.3074 (1377/4480, Estonian)
A=0.3417 (1317/3854, ALSPAC)
A=0.3484 (1292/3708, TWINSUK)
A=0.1174 (344/2930, KOREAN)
A=0.1660 (310/1868, HapMap)
A=0.343 (342/998, GoNL)
A=0.277 (166/600, NorthernSweden)
A=0.143 (70/490, SGDP_PRJ)
A=0.218 (47/216, Qatari)
A=0.052 (11/212, Vietnamese)
G=0.45 (38/84, Ancient Sardinia)
A=0.14 (8/56, Siberian)
A=0.33 (13/40, 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 37650 A=0.31923 G=0.68077
European Sub 27834 A=0.34239 G=0.65761
African Sub 3846 A=0.1466 G=0.8534
African Others Sub 136 A=0.154 G=0.846
African American Sub 3710 A=0.1464 G=0.8536
Asian Sub 176 A=0.193 G=0.807
East Asian Sub 116 A=0.147 G=0.853
Other Asian Sub 60 A=0.28 G=0.72
Latin American 1 Sub 314 A=0.287 G=0.713
Latin American 2 Sub 2850 A=0.3337 G=0.6663
South Asian Sub 126 A=0.175 G=0.825
Other Sub 2504 A=0.3307 G=0.6693


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=0.275662 G=0.724338
gnomAD - Genomes Global Study-wide 140094 A=0.273716 G=0.726284
gnomAD - Genomes European Sub 75878 A=0.33798 G=0.66202
gnomAD - Genomes African Sub 41970 A=0.14460 G=0.85540
gnomAD - Genomes American Sub 13640 A=0.32903 G=0.67097
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.3550 G=0.6450
gnomAD - Genomes East Asian Sub 3130 A=0.1319 G=0.8681
gnomAD - Genomes Other Sub 2152 A=0.2560 G=0.7440
Allele Frequency Aggregator Total Global 37650 A=0.31923 G=0.68077
Allele Frequency Aggregator European Sub 27834 A=0.34239 G=0.65761
Allele Frequency Aggregator African Sub 3846 A=0.1466 G=0.8534
Allele Frequency Aggregator Latin American 2 Sub 2850 A=0.3337 G=0.6663
Allele Frequency Aggregator Other Sub 2504 A=0.3307 G=0.6693
Allele Frequency Aggregator Latin American 1 Sub 314 A=0.287 G=0.713
Allele Frequency Aggregator Asian Sub 176 A=0.193 G=0.807
Allele Frequency Aggregator South Asian Sub 126 A=0.175 G=0.825
14KJPN JAPANESE Study-wide 28258 A=0.12704 G=0.87296
8.3KJPN JAPANESE Study-wide 16760 A=0.13013 G=0.86987
1000Genomes_30x Global Study-wide 6404 A=0.2032 G=0.7968
1000Genomes_30x African Sub 1786 A=0.1120 G=0.8880
1000Genomes_30x Europe Sub 1266 A=0.3428 G=0.6572
1000Genomes_30x South Asian Sub 1202 A=0.1581 G=0.8419
1000Genomes_30x East Asian Sub 1170 A=0.1385 G=0.8615
1000Genomes_30x American Sub 980 A=0.321 G=0.679
1000Genomes Global Study-wide 5008 A=0.2013 G=0.7987
1000Genomes African Sub 1322 A=0.1097 G=0.8903
1000Genomes East Asian Sub 1008 A=0.1379 G=0.8621
1000Genomes Europe Sub 1006 A=0.3360 G=0.6640
1000Genomes South Asian Sub 978 A=0.165 G=0.835
1000Genomes American Sub 694 A=0.324 G=0.676
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.3074 G=0.6926
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.3417 G=0.6583
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.3484 G=0.6516
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.1174 C=0.0000, G=0.8826
HapMap Global Study-wide 1868 A=0.1660 G=0.8340
HapMap American Sub 758 A=0.211 G=0.789
HapMap African Sub 690 A=0.101 G=0.899
HapMap Asian Sub 250 A=0.100 G=0.900
HapMap Europe Sub 170 A=0.324 G=0.676
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.343 G=0.657
Northern Sweden ACPOP Study-wide 600 A=0.277 G=0.723
SGDP_PRJ Global Study-wide 490 A=0.143 G=0.857
Qatari Global Study-wide 216 A=0.218 G=0.782
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.052 G=0.948
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 84 A=0.55 G=0.45
Siberian Global Study-wide 56 A=0.14 G=0.86
The Danish reference pan genome Danish Study-wide 40 A=0.33 G=0.68
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 1 NC_000001.11:g.20266382A>C
GRCh38.p14 chr 1 NC_000001.11:g.20266382A>G
GRCh37.p13 chr 1 NC_000001.10:g.20592875A>C
GRCh37.p13 chr 1 NC_000001.10:g.20592875A>G
LOC126805649 genomic region NG_081973.1:g.747A>C
LOC126805649 genomic region NG_081973.1:g.747A>G
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= C G
GRCh38.p14 chr 1 NC_000001.11:g.20266382= NC_000001.11:g.20266382A>C NC_000001.11:g.20266382A>G
GRCh37.p13 chr 1 NC_000001.10:g.20592875= NC_000001.10:g.20592875A>C NC_000001.10:g.20592875A>G
LOC126805649 genomic region NG_081973.1:g.747= NG_081973.1:g.747A>C NG_081973.1:g.747A>G
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#.

97 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss93295 Oct 10, 2002 (108)
2 SC_JCM ss5818540 Feb 20, 2003 (111)
3 BCM_SSAHASNP ss9821423 Jul 11, 2003 (116)
4 SC_JCM ss13503404 Dec 05, 2003 (123)
5 BCM_SSAHASNP ss13538006 Dec 05, 2003 (123)
6 PERLEGEN ss16333712 Feb 28, 2004 (123)
7 CSHL-HAPMAP ss16400636 Feb 27, 2004 (123)
8 SSAHASNP ss20584208 Apr 05, 2004 (123)
9 PERLEGEN ss24236374 Sep 20, 2004 (123)
10 ABI ss43859440 Mar 14, 2006 (126)
11 AFFY ss65919810 Dec 01, 2006 (127)
12 AFFY ss66507027 Dec 01, 2006 (127)
13 AFFY ss76329844 Dec 06, 2007 (129)
14 HGSV ss78472185 Dec 06, 2007 (129)
15 KRIBB_YJKIM ss81977929 Dec 15, 2007 (130)
16 HGSV ss85619236 Dec 15, 2007 (130)
17 BCMHGSC_JDW ss87281472 Mar 23, 2008 (129)
18 HUMANGENOME_JCVI ss99192211 Feb 06, 2009 (130)
19 BGI ss102725500 Feb 23, 2009 (131)
20 1000GENOMES ss108044842 Jan 22, 2009 (130)
21 1000GENOMES ss110152799 Jan 24, 2009 (130)
22 ILLUMINA-UK ss118547737 Feb 14, 2009 (130)
23 ENSEMBL ss137833071 Dec 01, 2009 (131)
24 ENSEMBL ss139090738 Dec 01, 2009 (131)
25 GMI ss154733996 Dec 01, 2009 (131)
26 COMPLETE_GENOMICS ss163154443 Jul 04, 2010 (132)
27 COMPLETE_GENOMICS ss163935805 Jul 04, 2010 (132)
28 COMPLETE_GENOMICS ss166203250 Jul 04, 2010 (132)
29 AFFY ss173282377 Jul 04, 2010 (132)
30 BUSHMAN ss198131650 Jul 04, 2010 (132)
31 BCM-HGSC-SUB ss205290337 Jul 04, 2010 (132)
32 1000GENOMES ss218272213 Jul 14, 2010 (132)
33 1000GENOMES ss230453642 Jul 14, 2010 (132)
34 1000GENOMES ss238163550 Jul 15, 2010 (132)
35 BL ss252966466 May 09, 2011 (134)
36 GMI ss275744477 May 04, 2012 (137)
37 GMI ss284014309 Apr 25, 2013 (138)
38 PJP ss290781536 May 09, 2011 (134)
39 ILLUMINA ss479184424 May 04, 2012 (137)
40 ILLUMINA ss482206646 May 04, 2012 (137)
41 ILLUMINA ss532776769 Sep 08, 2015 (146)
42 TISHKOFF ss553866656 Apr 25, 2013 (138)
43 SSMP ss647625344 Apr 25, 2013 (138)
44 ILLUMINA ss779539349 Aug 21, 2014 (142)
45 ILLUMINA ss780918180 Aug 21, 2014 (142)
46 ILLUMINA ss835010056 Aug 21, 2014 (142)
47 EVA-GONL ss974923669 Aug 21, 2014 (142)
48 JMKIDD_LAB ss1067719152 Aug 21, 2014 (142)
49 1000GENOMES ss1289948731 Aug 21, 2014 (142)
50 DDI ss1425737917 Apr 01, 2015 (144)
51 EVA_GENOME_DK ss1573927296 Apr 01, 2015 (144)
52 EVA_DECODE ss1584281841 Apr 01, 2015 (144)
53 EVA_UK10K_ALSPAC ss1599681663 Apr 01, 2015 (144)
54 EVA_UK10K_TWINSUK ss1642675696 Apr 01, 2015 (144)
55 EVA_SVP ss1712316278 Apr 01, 2015 (144)
56 HAMMER_LAB ss1794026434 Sep 08, 2015 (146)
57 WEILL_CORNELL_DGM ss1918135457 Feb 12, 2016 (147)
58 GENOMED ss1966700265 Jul 19, 2016 (147)
59 JJLAB ss2019579387 Sep 14, 2016 (149)
60 USC_VALOUEV ss2147582879 Dec 20, 2016 (150)
61 HUMAN_LONGEVITY ss2160546884 Dec 20, 2016 (150)
62 SYSTEMSBIOZJU ss2624305979 Nov 08, 2017 (151)
63 ILLUMINA ss2632486899 Nov 08, 2017 (151)
64 GRF ss2697487387 Nov 08, 2017 (151)
65 GNOMAD ss2752413889 Nov 08, 2017 (151)
66 SWEGEN ss2986429109 Nov 08, 2017 (151)
67 BIOINF_KMB_FNS_UNIBA ss3023554779 Nov 08, 2017 (151)
68 CSHL ss3343356561 Nov 08, 2017 (151)
69 ILLUMINA ss3626042951 Oct 11, 2018 (152)
70 ILLUMINA ss3630524706 Oct 11, 2018 (152)
71 ILLUMINA ss3641576644 Oct 11, 2018 (152)
72 URBANLAB ss3646616868 Oct 11, 2018 (152)
73 EGCUT_WGS ss3654499388 Jul 12, 2019 (153)
74 EVA_DECODE ss3686300386 Jul 12, 2019 (153)
75 ACPOP ss3726850107 Jul 12, 2019 (153)
76 EVA ss3745913707 Jul 12, 2019 (153)
77 KHV_HUMAN_GENOMES ss3798933956 Jul 12, 2019 (153)
78 EVA ss3826059243 Apr 25, 2020 (154)
79 EVA ss3836417652 Apr 25, 2020 (154)
80 EVA ss3841822076 Apr 25, 2020 (154)
81 SGDP_PRJ ss3848359361 Apr 25, 2020 (154)
82 KRGDB ss3893267707 Apr 25, 2020 (154)
83 EVA ss3984782829 Apr 26, 2021 (155)
84 TOPMED ss4441379137 Apr 26, 2021 (155)
85 TOMMO_GENOMICS ss5142823299 Apr 26, 2021 (155)
86 1000G_HIGH_COVERAGE ss5241429926 Oct 12, 2022 (156)
87 EVA ss5314598834 Oct 12, 2022 (156)
88 EVA ss5317194325 Oct 12, 2022 (156)
89 HUGCELL_USP ss5442588378 Oct 12, 2022 (156)
90 1000G_HIGH_COVERAGE ss5513301191 Oct 12, 2022 (156)
91 SANFORD_IMAGENETICS ss5625069129 Oct 12, 2022 (156)
92 TOMMO_GENOMICS ss5667227041 Oct 12, 2022 (156)
93 YY_MCH ss5800392561 Oct 12, 2022 (156)
94 EVA ss5831637749 Oct 12, 2022 (156)
95 EVA ss5848813833 Oct 12, 2022 (156)
96 EVA ss5907307696 Oct 12, 2022 (156)
97 EVA ss5936884470 Oct 12, 2022 (156)
98 1000Genomes NC_000001.10 - 20592875 Oct 11, 2018 (152)
99 1000Genomes_30x NC_000001.11 - 20266382 Oct 12, 2022 (156)
100 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 20592875 Oct 11, 2018 (152)
101 Genetic variation in the Estonian population NC_000001.10 - 20592875 Oct 11, 2018 (152)
102 The Danish reference pan genome NC_000001.10 - 20592875 Apr 25, 2020 (154)
103 gnomAD - Genomes NC_000001.11 - 20266382 Apr 26, 2021 (155)
104 Genome of the Netherlands Release 5 NC_000001.10 - 20592875 Apr 25, 2020 (154)
105 HapMap NC_000001.11 - 20266382 Apr 25, 2020 (154)
106 KOREAN population from KRGDB NC_000001.10 - 20592875 Apr 25, 2020 (154)
107 Northern Sweden NC_000001.10 - 20592875 Jul 12, 2019 (153)
108 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 20592875 Apr 26, 2021 (155)
109 Qatari NC_000001.10 - 20592875 Apr 25, 2020 (154)
110 SGDP_PRJ NC_000001.10 - 20592875 Apr 25, 2020 (154)
111 Siberian NC_000001.10 - 20592875 Apr 25, 2020 (154)
112 8.3KJPN NC_000001.10 - 20592875 Apr 26, 2021 (155)
113 14KJPN NC_000001.11 - 20266382 Oct 12, 2022 (156)
114 TopMed NC_000001.11 - 20266382 Apr 26, 2021 (155)
115 UK 10K study - Twins NC_000001.10 - 20592875 Oct 11, 2018 (152)
116 A Vietnamese Genetic Variation Database NC_000001.10 - 20592875 Jul 12, 2019 (153)
117 ALFA NC_000001.11 - 20266382 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)
rs9287032 Sep 24, 2004 (123)
rs11564785 Sep 24, 2004 (123)
rs17355062 Oct 07, 2004 (123)
rs60245293 May 25, 2008 (130)
rs60806201 Feb 27, 2009 (130)
rs74228489 Dec 02, 2009 (131)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
445101, ss3893267707 NC_000001.10:20592874:A:C NC_000001.11:20266381:A:C (self)
ss78472185, ss85619236 NC_000001.8:20338180:A:G NC_000001.11:20266381:A:G (self)
ss87281472, ss108044842, ss110152799, ss118547737, ss163154443, ss163935805, ss166203250, ss198131650, ss205290337, ss252966466, ss275744477, ss284014309, ss290781536, ss482206646, ss1584281841, ss1712316278 NC_000001.9:20465461:A:G NC_000001.11:20266381:A:G (self)
633636, 333501, 237636, 1417063, 144943, 445101, 134972, 8756, 177387, 376341, 99233, 792606, 333501, 71590, ss218272213, ss230453642, ss238163550, ss479184424, ss532776769, ss553866656, ss647625344, ss779539349, ss780918180, ss835010056, ss974923669, ss1067719152, ss1289948731, ss1425737917, ss1573927296, ss1599681663, ss1642675696, ss1794026434, ss1918135457, ss1966700265, ss2019579387, ss2147582879, ss2624305979, ss2632486899, ss2697487387, ss2752413889, ss2986429109, ss3343356561, ss3626042951, ss3630524706, ss3641576644, ss3654499388, ss3726850107, ss3745913707, ss3826059243, ss3836417652, ss3848359361, ss3893267707, ss3984782829, ss5142823299, ss5314598834, ss5317194325, ss5625069129, ss5831637749, ss5936884470 NC_000001.10:20592874:A:G NC_000001.11:20266381:A:G (self)
827126, 4399382, 26035, 1064145, 4985472, 10283555958, ss2160546884, ss3023554779, ss3646616868, ss3686300386, ss3798933956, ss3841822076, ss4441379137, ss5241429926, ss5442588378, ss5513301191, ss5667227041, ss5800392561, ss5848813833, ss5907307696 NC_000001.11:20266381:A:G NC_000001.11:20266381:A:G (self)
ss9821423 NT_004610.15:1396124:A:G NC_000001.11:20266381:A:G (self)
ss13503404, ss13538006, ss16400636, ss20584208 NT_004610.16:1396124:A:G NC_000001.11:20266381:A:G (self)
ss93295, ss5818540, ss16333712, ss24236374, ss43859440, ss65919810, ss66507027, ss76329844, ss81977929, ss99192211, ss102725500, ss137833071, ss139090738, ss154733996, ss173282377 NT_004610.19:7272962:A:G NC_000001.11:20266381:A:G (self)
Help

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

No publications for rs3888820

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