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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.

rs12068388

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:26295105 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.486596 (128797/264690, TOPMED)
G=0.465627 (65104/139820, GnomAD)
A=0.27426 (7750/28258, 14KJPN) (+ 18 more)
G=0.42715 (7681/17982, ALFA)
A=0.27488 (4607/16760, 8.3KJPN)
A=0.3910 (2504/6404, 1000G_30x)
A=0.3846 (1926/5008, 1000G)
G=0.3757 (1683/4480, Estonian)
G=0.3480 (1341/3854, ALSPAC)
G=0.3436 (1274/3708, TWINSUK)
A=0.2881 (844/2930, KOREAN)
A=0.2898 (531/1832, Korea1K)
G=0.353 (352/998, GoNL)
A=0.302 (231/764, PRJEB37584)
G=0.375 (225/600, NorthernSweden)
A=0.479 (157/328, HapMap)
G=0.335 (108/322, SGDP_PRJ)
A=0.481 (104/216, Qatari)
A=0.234 (50/214, Vietnamese)
G=0.36 (15/42, Siberian)
G=0.35 (14/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
UBXN11 : 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 17982 G=0.42715 A=0.57285, C=0.00000
European Sub 13724 G=0.36957 A=0.63043, C=0.00000
African Sub 2604 G=0.6467 A=0.3533, C=0.0000
African Others Sub 102 G=0.696 A=0.304, C=0.000
African American Sub 2502 G=0.6447 A=0.3553, C=0.0000
Asian Sub 112 G=0.714 A=0.286, C=0.000
East Asian Sub 86 G=0.72 A=0.28, C=0.00
Other Asian Sub 26 G=0.69 A=0.31, C=0.00
Latin American 1 Sub 146 G=0.534 A=0.466, C=0.000
Latin American 2 Sub 610 G=0.566 A=0.434, C=0.000
South Asian Sub 98 G=0.78 A=0.22, C=0.00
Other Sub 688 G=0.503 A=0.497, C=0.000


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 G=0.486596 A=0.513404
gnomAD - Genomes Global Study-wide 139820 G=0.465627 A=0.534373
gnomAD - Genomes European Sub 75786 G=0.36268 A=0.63732
gnomAD - Genomes African Sub 41828 G=0.61777 A=0.38223
gnomAD - Genomes American Sub 13620 G=0.52981 A=0.47019
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.3837 A=0.6163
gnomAD - Genomes East Asian Sub 3120 G=0.7192 A=0.2808
gnomAD - Genomes Other Sub 2148 G=0.4865 A=0.5135
14KJPN JAPANESE Study-wide 28258 G=0.72574 A=0.27426
Allele Frequency Aggregator Total Global 17982 G=0.42715 A=0.57285, C=0.00000
Allele Frequency Aggregator European Sub 13724 G=0.36957 A=0.63043, C=0.00000
Allele Frequency Aggregator African Sub 2604 G=0.6467 A=0.3533, C=0.0000
Allele Frequency Aggregator Other Sub 688 G=0.503 A=0.497, C=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.566 A=0.434, C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.534 A=0.466, C=0.000
Allele Frequency Aggregator Asian Sub 112 G=0.714 A=0.286, C=0.000
Allele Frequency Aggregator South Asian Sub 98 G=0.78 A=0.22, C=0.00
8.3KJPN JAPANESE Study-wide 16760 G=0.72512 A=0.27488
1000Genomes_30x Global Study-wide 6404 G=0.6090 A=0.3910
1000Genomes_30x African Sub 1786 G=0.6775 A=0.3225
1000Genomes_30x Europe Sub 1266 G=0.3570 A=0.6430
1000Genomes_30x South Asian Sub 1202 G=0.7072 A=0.2928
1000Genomes_30x East Asian Sub 1170 G=0.6803 A=0.3197
1000Genomes_30x American Sub 980 G=0.604 A=0.396
1000Genomes Global Study-wide 5008 G=0.6154 A=0.3846
1000Genomes African Sub 1322 G=0.6755 A=0.3245
1000Genomes East Asian Sub 1008 G=0.6855 A=0.3145
1000Genomes Europe Sub 1006 G=0.3718 A=0.6282
1000Genomes South Asian Sub 978 G=0.719 A=0.281
1000Genomes American Sub 694 G=0.607 A=0.393
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.3757 A=0.6243
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.3480 A=0.6520
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.3436 A=0.6564
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7119 A=0.2881
Korean Genome Project KOREAN Study-wide 1832 G=0.7102 A=0.2898
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.353 A=0.647
CNV burdens in cranial meningiomas Global Study-wide 764 G=0.698 A=0.302
CNV burdens in cranial meningiomas CRM Sub 764 G=0.698 A=0.302
Northern Sweden ACPOP Study-wide 600 G=0.375 A=0.625
HapMap Global Study-wide 328 G=0.521 A=0.479
HapMap African Sub 120 G=0.608 A=0.392
HapMap American Sub 118 G=0.263 A=0.737
HapMap Asian Sub 90 G=0.74 A=0.26
SGDP_PRJ Global Study-wide 322 G=0.335 A=0.665
Qatari Global Study-wide 216 G=0.519 A=0.481
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.766 A=0.234
Siberian Global Study-wide 42 G=0.36 A=0.64
The Danish reference pan genome Danish Study-wide 40 G=0.35 A=0.65
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.26295105G>A
GRCh38.p14 chr 1 NC_000001.11:g.26295105G>C
GRCh37.p13 chr 1 NC_000001.10:g.26621596G>A
GRCh37.p13 chr 1 NC_000001.10:g.26621596G>C
UBXN11 RefSeqGene NG_028986.1:g.28161C>T
UBXN11 RefSeqGene NG_028986.1:g.28161C>G
Gene: UBXN11, UBX domain protein 11 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
UBXN11 transcript variant 3 NM_001077262.2:c.199+5821…

NM_001077262.2:c.199+5821C>T

N/A Intron Variant
UBXN11 transcript variant 4 NM_001389556.1:c.433-774C…

NM_001389556.1:c.433-774C>T

N/A Intron Variant
UBXN11 transcript variant 5 NM_001389559.1:c.334-774C…

NM_001389559.1:c.334-774C>T

N/A Intron Variant
UBXN11 transcript variant 1 NM_145345.3:c.334-774C>T N/A Intron Variant
UBXN11 transcript variant 2 NM_183008.3:c.433-774C>T 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 G= A C
GRCh38.p14 chr 1 NC_000001.11:g.26295105= NC_000001.11:g.26295105G>A NC_000001.11:g.26295105G>C
GRCh37.p13 chr 1 NC_000001.10:g.26621596= NC_000001.10:g.26621596G>A NC_000001.10:g.26621596G>C
UBXN11 RefSeqGene NG_028986.1:g.28161= NG_028986.1:g.28161C>T NG_028986.1:g.28161C>G
UBXN11 transcript variant 3 NM_001077262.1:c.199+5821= NM_001077262.1:c.199+5821C>T NM_001077262.1:c.199+5821C>G
UBXN11 transcript variant 3 NM_001077262.2:c.199+5821= NM_001077262.2:c.199+5821C>T NM_001077262.2:c.199+5821C>G
UBXN11 transcript variant 4 NM_001389556.1:c.433-774= NM_001389556.1:c.433-774C>T NM_001389556.1:c.433-774C>G
UBXN11 transcript variant 5 NM_001389559.1:c.334-774= NM_001389559.1:c.334-774C>T NM_001389559.1:c.334-774C>G
UBXN11 transcript variant 1 NM_145345.2:c.334-774= NM_145345.2:c.334-774C>T NM_145345.2:c.334-774C>G
UBXN11 transcript variant 1 NM_145345.3:c.334-774= NM_145345.3:c.334-774C>T NM_145345.3:c.334-774C>G
UBXN11 transcript variant 2 NM_183008.2:c.433-774= NM_183008.2:c.433-774C>T NM_183008.2:c.433-774C>G
UBXN11 transcript variant 2 NM_183008.3:c.433-774= NM_183008.3:c.433-774C>T NM_183008.3:c.433-774C>G
UBXN11 transcript variant X1 XM_005246030.1:c.334-774= XM_005246030.1:c.334-774C>T XM_005246030.1:c.334-774C>G
UBXN11 transcript variant X2 XM_005246031.1:c.319-774= XM_005246031.1:c.319-774C>T XM_005246031.1:c.319-774C>G
UBXN11 transcript variant X3 XM_005246032.1:c.319-774= XM_005246032.1:c.319-774C>T XM_005246032.1:c.319-774C>G
UBXN11 transcript variant X4 XM_005246033.1:c.319-774= XM_005246033.1:c.319-774C>T XM_005246033.1:c.319-774C>G
UBXN11 transcript variant X5 XM_005246034.1:c.208-774= XM_005246034.1:c.208-774C>T XM_005246034.1:c.208-774C>G
UBXN11 transcript variant X6 XM_005246035.1:c.208-774= XM_005246035.1:c.208-774C>T XM_005246035.1:c.208-774C>G
UBXN11 transcript variant X7 XM_005246036.1:c.-42-774= XM_005246036.1:c.-42-774C>T XM_005246036.1:c.-42-774C>G
UBXN11 transcript variant X8 XM_005246037.1:c.-42-774= XM_005246037.1:c.-42-774C>T XM_005246037.1:c.-42-774C>G
UBXN11 transcript variant X9 XM_005246038.1:c.-168+1814= XM_005246038.1:c.-168+1814C>T XM_005246038.1:c.-168+1814C>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#.

64 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18156835 Feb 28, 2004 (120)
2 SSAHASNP ss20441252 Apr 05, 2004 (121)
3 HUMANGENOME_JCVI ss97926930 Feb 06, 2009 (130)
4 1000GENOMES ss108076306 Jan 22, 2009 (130)
5 ENSEMBL ss143235369 Dec 01, 2009 (131)
6 COMPLETE_GENOMICS ss164008147 Jul 04, 2010 (132)
7 COMPLETE_GENOMICS ss166271211 Jul 04, 2010 (132)
8 1000GENOMES ss218293170 Jul 14, 2010 (132)
9 1000GENOMES ss230468928 Jul 14, 2010 (132)
10 1000GENOMES ss238175084 Jul 15, 2010 (132)
11 GMI ss275760362 May 04, 2012 (137)
12 GMI ss284022570 Apr 25, 2013 (138)
13 PJP ss290794192 May 09, 2011 (134)
14 TISHKOFF ss553914408 Apr 25, 2013 (138)
15 SSMP ss647652045 Apr 25, 2013 (138)
16 EVA-GONL ss974966676 Aug 21, 2014 (142)
17 JMKIDD_LAB ss1067748634 Aug 21, 2014 (142)
18 1000GENOMES ss1290116202 Aug 21, 2014 (142)
19 DDI ss1425752662 Apr 01, 2015 (144)
20 EVA_GENOME_DK ss1573952361 Apr 01, 2015 (144)
21 EVA_DECODE ss1584325758 Apr 01, 2015 (144)
22 EVA_UK10K_ALSPAC ss1599768084 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1642762117 Apr 01, 2015 (144)
24 WEILL_CORNELL_DGM ss1918178946 Feb 12, 2016 (147)
25 GENOMED ss1966709025 Jul 19, 2016 (147)
26 JJLAB ss2019601137 Sep 14, 2016 (149)
27 USC_VALOUEV ss2147607578 Dec 20, 2016 (150)
28 HUMAN_LONGEVITY ss2160887801 Dec 20, 2016 (150)
29 SYSTEMSBIOZJU ss2624317743 Nov 08, 2017 (151)
30 GRF ss2697513327 Nov 08, 2017 (151)
31 GNOMAD ss2752901741 Nov 08, 2017 (151)
32 SWEGEN ss2986499446 Nov 08, 2017 (151)
33 BIOINF_KMB_FNS_UNIBA ss3023566220 Nov 08, 2017 (151)
34 CSHL ss3343375824 Nov 08, 2017 (151)
35 URBANLAB ss3646627550 Oct 11, 2018 (152)
36 EGCUT_WGS ss3654564632 Jul 12, 2019 (153)
37 EVA_DECODE ss3686388311 Jul 12, 2019 (153)
38 ACPOP ss3726885629 Jul 12, 2019 (153)
39 EVA ss3745964738 Jul 12, 2019 (153)
40 PACBIO ss3783359396 Jul 12, 2019 (153)
41 PACBIO ss3789027931 Jul 12, 2019 (153)
42 PACBIO ss3793900439 Jul 12, 2019 (153)
43 KHV_HUMAN_GENOMES ss3798985370 Jul 12, 2019 (153)
44 EVA ss3826081528 Apr 25, 2020 (154)
45 EVA ss3836428791 Apr 25, 2020 (154)
46 EVA ss3841833618 Apr 25, 2020 (154)
47 SGDP_PRJ ss3848452545 Apr 25, 2020 (154)
48 KRGDB ss3893374415 Apr 25, 2020 (154)
49 KOGIC ss3944081749 Apr 25, 2020 (154)
50 EVA ss3984454178 Apr 27, 2021 (155)
51 TOPMED ss4442835861 Apr 27, 2021 (155)
52 TOMMO_GENOMICS ss5143027587 Apr 27, 2021 (155)
53 1000G_HIGH_COVERAGE ss5241581930 Oct 13, 2022 (156)
54 EVA ss5317467638 Oct 13, 2022 (156)
55 HUGCELL_USP ss5442723699 Oct 13, 2022 (156)
56 EVA ss5505794771 Oct 13, 2022 (156)
57 1000G_HIGH_COVERAGE ss5513524815 Oct 13, 2022 (156)
58 SANFORD_IMAGENETICS ss5625152393 Oct 13, 2022 (156)
59 TOMMO_GENOMICS ss5667500018 Oct 13, 2022 (156)
60 YY_MCH ss5800429809 Oct 13, 2022 (156)
61 EVA ss5831697431 Oct 13, 2022 (156)
62 EVA ss5848830713 Oct 13, 2022 (156)
63 EVA ss5907478054 Oct 13, 2022 (156)
64 EVA ss5936968965 Oct 13, 2022 (156)
65 1000Genomes NC_000001.10 - 26621596 Oct 11, 2018 (152)
66 1000Genomes_30x NC_000001.11 - 26295105 Oct 13, 2022 (156)
67 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 26621596 Oct 11, 2018 (152)
68 Genetic variation in the Estonian population NC_000001.10 - 26621596 Oct 11, 2018 (152)
69 The Danish reference pan genome NC_000001.10 - 26621596 Apr 25, 2020 (154)
70 gnomAD - Genomes NC_000001.11 - 26295105 Apr 27, 2021 (155)
71 Genome of the Netherlands Release 5 NC_000001.10 - 26621596 Apr 25, 2020 (154)
72 HapMap NC_000001.11 - 26295105 Apr 25, 2020 (154)
73 KOREAN population from KRGDB NC_000001.10 - 26621596 Apr 25, 2020 (154)
74 Korean Genome Project NC_000001.11 - 26295105 Apr 25, 2020 (154)
75 Northern Sweden NC_000001.10 - 26621596 Jul 12, 2019 (153)
76 CNV burdens in cranial meningiomas NC_000001.10 - 26621596 Apr 27, 2021 (155)
77 Qatari NC_000001.10 - 26621596 Apr 25, 2020 (154)
78 SGDP_PRJ NC_000001.10 - 26621596 Apr 25, 2020 (154)
79 Siberian NC_000001.10 - 26621596 Apr 25, 2020 (154)
80 8.3KJPN NC_000001.10 - 26621596 Apr 27, 2021 (155)
81 14KJPN NC_000001.11 - 26295105 Oct 13, 2022 (156)
82 TopMed NC_000001.11 - 26295105 Apr 27, 2021 (155)
83 UK 10K study - Twins NC_000001.10 - 26621596 Oct 11, 2018 (152)
84 A Vietnamese Genetic Variation Database NC_000001.10 - 26621596 Jul 12, 2019 (153)
85 ALFA NC_000001.11 - 26295105 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss108076306, ss164008147, ss166271211, ss275760362, ss284022570, ss290794192, ss1584325758 NC_000001.9:26494182:G:A NC_000001.11:26295104:G:A (self)
807115, 429586, 302880, 1433013, 185768, 551809, 170494, 3480, 220876, 469525, 123932, 996894, 429586, 90102, ss218293170, ss230468928, ss238175084, ss553914408, ss647652045, ss974966676, ss1067748634, ss1290116202, ss1425752662, ss1573952361, ss1599768084, ss1642762117, ss1918178946, ss1966709025, ss2019601137, ss2147607578, ss2624317743, ss2697513327, ss2752901741, ss2986499446, ss3343375824, ss3654564632, ss3726885629, ss3745964738, ss3783359396, ss3789027931, ss3793900439, ss3826081528, ss3836428791, ss3848452545, ss3893374415, ss3984454178, ss5143027587, ss5317467638, ss5505794771, ss5625152393, ss5831697431, ss5936968965 NC_000001.10:26621595:G:A NC_000001.11:26295104:G:A (self)
1050750, 5645538, 33565, 459750, 1337122, 6442196, 1066477341, ss2160887801, ss3023566220, ss3646627550, ss3686388311, ss3798985370, ss3841833618, ss3944081749, ss4442835861, ss5241581930, ss5442723699, ss5513524815, ss5667500018, ss5800429809, ss5848830713, ss5907478054 NC_000001.11:26295104:G:A NC_000001.11:26295104:G:A (self)
ss97926930, ss143235369 NT_004610.19:13301683:G:A NC_000001.11:26295104:G:A (self)
ss18156835, ss20441252 NT_037485.3:732804:G:A NC_000001.11:26295104:G:A (self)
1066477341 NC_000001.11:26295104:G:C NC_000001.11:26295104:G:C (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 rs12068388

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