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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.

rs5771238

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr22:50214117 (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=0.077547 (20526/264690, TOPMED)
G=0.075915 (10629/140012, GnomAD)
G=0.07989 (2970/37178, ALFA) (+ 17 more)
G=0.28555 (8069/28258, 14KJPN)
G=0.28109 (4711/16760, 8.3KJPN)
G=0.1181 (756/6404, 1000G_30x)
G=0.1258 (630/5008, 1000G)
G=0.0830 (372/4480, Estonian)
G=0.0732 (282/3854, ALSPAC)
G=0.0742 (275/3708, TWINSUK)
G=0.3065 (898/2930, KOREAN)
G=0.3122 (572/1832, Korea1K)
G=0.068 (68/998, GoNL)
G=0.052 (31/600, NorthernSweden)
G=0.097 (21/216, Qatari)
G=0.411 (88/214, Vietnamese)
A=0.418 (51/122, SGDP_PRJ)
G=0.05 (2/40, GENOME_DK)
A=0.50 (8/16, Siberian)
G=0.50 (8/16, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SELENOO : 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 37272 A=0.91997 G=0.08003
European Sub 30876 A=0.91916 G=0.08084
African Sub 3168 A=0.9539 G=0.0461
African Others Sub 124 A=0.927 G=0.073
African American Sub 3044 A=0.9550 G=0.0450
Asian Sub 128 A=0.664 G=0.336
East Asian Sub 100 A=0.69 G=0.31
Other Asian Sub 28 A=0.57 G=0.43
Latin American 1 Sub 168 A=0.923 G=0.077
Latin American 2 Sub 700 A=0.957 G=0.043
South Asian Sub 114 A=0.868 G=0.132
Other Sub 2118 A=0.8867 G=0.1133


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=0.922453 G=0.077547
gnomAD - Genomes Global Study-wide 140012 A=0.924085 G=0.075915
gnomAD - Genomes European Sub 75882 A=0.92053 G=0.07947
gnomAD - Genomes African Sub 41924 A=0.95132 G=0.04868
gnomAD - Genomes American Sub 13628 A=0.94365 G=0.05635
gnomAD - Genomes Ashkenazi Jewish Sub 3316 A=0.8344 G=0.1656
gnomAD - Genomes East Asian Sub 3118 A=0.6648 G=0.3352
gnomAD - Genomes Other Sub 2144 A=0.9086 G=0.0914
Allele Frequency Aggregator Total Global 37178 A=0.92011 G=0.07989
Allele Frequency Aggregator European Sub 30800 A=0.91932 G=0.08068
Allele Frequency Aggregator African Sub 3168 A=0.9539 G=0.0461
Allele Frequency Aggregator Other Sub 2100 A=0.8867 G=0.1133
Allele Frequency Aggregator Latin American 2 Sub 700 A=0.957 G=0.043
Allele Frequency Aggregator Latin American 1 Sub 168 A=0.923 G=0.077
Allele Frequency Aggregator Asian Sub 128 A=0.664 G=0.336
Allele Frequency Aggregator South Asian Sub 114 A=0.868 G=0.132
14KJPN JAPANESE Study-wide 28258 A=0.71445 G=0.28555
8.3KJPN JAPANESE Study-wide 16760 A=0.71891 G=0.28109
1000Genomes_30x Global Study-wide 6404 A=0.8819 G=0.1181
1000Genomes_30x African Sub 1786 A=0.9636 G=0.0364
1000Genomes_30x Europe Sub 1266 A=0.9265 G=0.0735
1000Genomes_30x South Asian Sub 1202 A=0.8735 G=0.1265
1000Genomes_30x East Asian Sub 1170 A=0.6590 G=0.3410
1000Genomes_30x American Sub 980 A=0.952 G=0.048
1000Genomes Global Study-wide 5008 A=0.8742 G=0.1258
1000Genomes African Sub 1322 A=0.9622 G=0.0378
1000Genomes East Asian Sub 1008 A=0.6607 G=0.3393
1000Genomes Europe Sub 1006 A=0.9294 G=0.0706
1000Genomes South Asian Sub 978 A=0.866 G=0.134
1000Genomes American Sub 694 A=0.948 G=0.052
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9170 G=0.0830
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9268 G=0.0732
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9258 G=0.0742
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.6935 G=0.3065
Korean Genome Project KOREAN Study-wide 1832 A=0.6878 G=0.3122
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.932 G=0.068
Northern Sweden ACPOP Study-wide 600 A=0.948 G=0.052
Qatari Global Study-wide 216 A=0.903 G=0.097
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.589 G=0.411
SGDP_PRJ Global Study-wide 122 A=0.418 G=0.582
The Danish reference pan genome Danish Study-wide 40 A=0.95 G=0.05
Siberian Global Study-wide 16 A=0.50 G=0.50
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 22 NC_000022.11:g.50214117A>G
GRCh37.p13 chr 22 NC_000022.10:g.50652546A>G
Gene: SELENOO, selenoprotein O (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SELENOO transcript NM_031454.2:c.1352-1600A>G N/A Intron Variant
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
GRCh38.p14 chr 22 NC_000022.11:g.50214117= NC_000022.11:g.50214117A>G
GRCh37.p13 chr 22 NC_000022.10:g.50652546= NC_000022.10:g.50652546A>G
SELENOO transcript NM_031454.1:c.1352-1600= NM_031454.1:c.1352-1600A>G
SELENOO transcript NM_031454.2:c.1352-1600= NM_031454.2:c.1352-1600A>G
SELO transcript variant X1 XM_005261939.1:c.392-1600= XM_005261939.1:c.392-1600A>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#.

61 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8025706 Apr 21, 2003 (114)
2 BGI ss103880681 Feb 23, 2009 (131)
3 1000GENOMES ss228743161 Jul 14, 2010 (132)
4 1000GENOMES ss238113368 Jul 15, 2010 (132)
5 1000GENOMES ss244221649 Jul 15, 2010 (132)
6 GMI ss283677461 May 04, 2012 (137)
7 ILLUMINA ss482878070 May 04, 2012 (137)
8 ILLUMINA ss484335822 May 04, 2012 (137)
9 ILLUMINA ss534802198 Sep 08, 2015 (146)
10 SSMP ss662648831 Apr 25, 2013 (138)
11 ILLUMINA ss780088997 Aug 21, 2014 (142)
12 ILLUMINA ss781907672 Aug 21, 2014 (142)
13 ILLUMINA ss835571214 Aug 21, 2014 (142)
14 EVA-GONL ss995472145 Aug 21, 2014 (142)
15 JMKIDD_LAB ss1082743478 Aug 21, 2014 (142)
16 1000GENOMES ss1367624880 Aug 21, 2014 (142)
17 DDI ss1429294452 Apr 01, 2015 (144)
18 EVA_GENOME_DK ss1579798267 Apr 01, 2015 (144)
19 EVA_UK10K_ALSPAC ss1640234134 Apr 01, 2015 (144)
20 EVA_UK10K_TWINSUK ss1683228167 Apr 01, 2015 (144)
21 EVA_DECODE ss1699541080 Apr 01, 2015 (144)
22 WEILL_CORNELL_DGM ss1939045758 Feb 12, 2016 (147)
23 JJLAB ss2030295115 Sep 14, 2016 (149)
24 USC_VALOUEV ss2158921048 Dec 20, 2016 (150)
25 HUMAN_LONGEVITY ss2248260395 Dec 20, 2016 (150)
26 SYSTEMSBIOZJU ss2629644447 Nov 08, 2017 (151)
27 ILLUMINA ss2633895901 Nov 08, 2017 (151)
28 GRF ss2704675335 Nov 08, 2017 (151)
29 GNOMAD ss2975678154 Nov 08, 2017 (151)
30 AFFY ss2985243536 Nov 08, 2017 (151)
31 AFFY ss2985860832 Nov 08, 2017 (151)
32 SWEGEN ss3019494532 Nov 08, 2017 (151)
33 BIOINF_KMB_FNS_UNIBA ss3028985870 Nov 08, 2017 (151)
34 CSHL ss3352894960 Nov 08, 2017 (151)
35 ILLUMINA ss3628563698 Oct 12, 2018 (152)
36 ILLUMINA ss3631845420 Oct 12, 2018 (152)
37 ILLUMINA ss3642226430 Oct 12, 2018 (152)
38 ILLUMINA ss3654011894 Oct 12, 2018 (152)
39 EGCUT_WGS ss3685982825 Jul 13, 2019 (153)
40 EVA_DECODE ss3708434223 Jul 13, 2019 (153)
41 ACPOP ss3744036243 Jul 13, 2019 (153)
42 EVA ss3759530133 Jul 13, 2019 (153)
43 KHV_HUMAN_GENOMES ss3822686069 Jul 13, 2019 (153)
44 EVA ss3836052255 Apr 27, 2020 (154)
45 SGDP_PRJ ss3890803261 Apr 27, 2020 (154)
46 KRGDB ss3941206649 Apr 27, 2020 (154)
47 KOGIC ss3983888813 Apr 27, 2020 (154)
48 TOPMED ss5113109872 Apr 27, 2021 (155)
49 TOMMO_GENOMICS ss5233172306 Apr 27, 2021 (155)
50 1000G_HIGH_COVERAGE ss5311515368 Oct 16, 2022 (156)
51 EVA ss5316067740 Oct 16, 2022 (156)
52 EVA ss5442056986 Oct 16, 2022 (156)
53 HUGCELL_USP ss5503314919 Oct 16, 2022 (156)
54 1000G_HIGH_COVERAGE ss5619251455 Oct 16, 2022 (156)
55 SANFORD_IMAGENETICS ss5664725286 Oct 16, 2022 (156)
56 TOMMO_GENOMICS ss5794469785 Oct 16, 2022 (156)
57 YY_MCH ss5818813932 Oct 16, 2022 (156)
58 EVA ss5822235622 Oct 16, 2022 (156)
59 EVA ss5853442710 Oct 16, 2022 (156)
60 EVA ss5882285396 Oct 16, 2022 (156)
61 EVA ss5959584710 Oct 16, 2022 (156)
62 1000Genomes NC_000022.10 - 50652546 Oct 12, 2018 (152)
63 1000Genomes_30x NC_000022.11 - 50214117 Oct 16, 2022 (156)
64 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 50652546 Oct 12, 2018 (152)
65 Genetic variation in the Estonian population NC_000022.10 - 50652546 Oct 12, 2018 (152)
66 The Danish reference pan genome NC_000022.10 - 50652546 Apr 27, 2020 (154)
67 gnomAD - Genomes NC_000022.11 - 50214117 Apr 27, 2021 (155)
68 Genome of the Netherlands Release 5 NC_000022.10 - 50652546 Apr 27, 2020 (154)
69 KOREAN population from KRGDB NC_000022.10 - 50652546 Apr 27, 2020 (154)
70 Korean Genome Project NC_000022.11 - 50214117 Apr 27, 2020 (154)
71 Northern Sweden NC_000022.10 - 50652546 Jul 13, 2019 (153)
72 Qatari NC_000022.10 - 50652546 Apr 27, 2020 (154)
73 SGDP_PRJ NC_000022.10 - 50652546 Apr 27, 2020 (154)
74 Siberian NC_000022.10 - 50652546 Apr 27, 2020 (154)
75 8.3KJPN NC_000022.10 - 50652546 Apr 27, 2021 (155)
76 14KJPN NC_000022.11 - 50214117 Oct 16, 2022 (156)
77 TopMed NC_000022.11 - 50214117 Apr 27, 2021 (155)
78 UK 10K study - Twins NC_000022.10 - 50652546 Oct 12, 2018 (152)
79 A Vietnamese Genetic Variation Database NC_000022.10 - 50652546 Jul 13, 2019 (153)
80 ALFA NC_000022.11 - 50214117 Apr 27, 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)
rs74280046 Dec 02, 2009 (131)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss283677461, ss484335822, ss1699541080 NC_000022.9:48994672:A:G NC_000022.11:50214116:A:G (self)
81193098, 44912437, 31721073, 5963206, 20010067, 48384043, 17321108, 21087680, 42820241, 11437402, 91141613, 44912437, 9903838, ss228743161, ss238113368, ss244221649, ss482878070, ss534802198, ss662648831, ss780088997, ss781907672, ss835571214, ss995472145, ss1082743478, ss1367624880, ss1429294452, ss1579798267, ss1640234134, ss1683228167, ss1939045758, ss2030295115, ss2158921048, ss2629644447, ss2633895901, ss2704675335, ss2975678154, ss2985243536, ss2985860832, ss3019494532, ss3352894960, ss3628563698, ss3631845420, ss3642226430, ss3654011894, ss3685982825, ss3744036243, ss3759530133, ss3836052255, ss3890803261, ss3941206649, ss5233172306, ss5316067740, ss5442056986, ss5664725286, ss5822235622, ss5959584710 NC_000022.10:50652545:A:G NC_000022.11:50214116:A:G (self)
106777390, 573227497, 40266814, 128306889, 388218819, 3088536977, ss2248260395, ss3028985870, ss3708434223, ss3822686069, ss3983888813, ss5113109872, ss5311515368, ss5503314919, ss5619251455, ss5794469785, ss5818813932, ss5853442710, ss5882285396 NC_000022.11:50214116:A:G NC_000022.11:50214116:A:G (self)
ss103880681 NT_011526.7:237768:A:G NC_000022.11:50214116:A:G (self)
ss8025706 NT_019197.3:227536:A:G NC_000022.11:50214116: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 rs5771238

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