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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.

rs12021502

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:77703073 (GRCh38.p13) 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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.063489 (9447/148798, ALFA)
A=0.12333 (2067/16760, 8.3KJPN)
A=0.0573 (287/5008, 1000G) (+ 14 more)
A=0.0824 (369/4480, Estonian)
A=0.0597 (230/3854, ALSPAC)
A=0.0618 (229/3708, TWINSUK)
A=0.1232 (361/2930, KOREAN)
A=0.0740 (97/1310, HapMap)
A=0.0739 (84/1136, Daghestan)
A=0.065 (65/998, GoNL)
A=0.055 (33/600, NorthernSweden)
A=0.032 (7/216, Qatari)
A=0.098 (21/214, Vietnamese)
C=0.48 (47/98, SGDP_PRJ)
A=0.03 (1/40, GENOME_DK)
C=0.50 (6/12, Siberian)
A=0.50 (6/12, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
USP33 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.77703073C>A
GRCh38.p13 chr 1 NC_000001.11:g.77703073C>T
GRCh37.p13 chr 1 NC_000001.10:g.78168758C>A
GRCh37.p13 chr 1 NC_000001.10:g.78168758C>T
Gene: USP33, ubiquitin specific peptidase 33 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
USP33 transcript variant 4 NM_001377430.1:c.2476-160…

NM_001377430.1:c.2476-1602G>T

N/A Intron Variant
USP33 transcript variant 5 NM_001377431.1:c.2383-160…

NM_001377431.1:c.2383-1602G>T

N/A Intron Variant
USP33 transcript variant 6 NM_001377432.1:c.2500-514…

NM_001377432.1:c.2500-5142G>T

N/A Intron Variant
USP33 transcript variant 7 NM_001377433.1:c.2203-160…

NM_001377433.1:c.2203-1602G>T

N/A Intron Variant
USP33 transcript variant 8 NM_001377434.1:c.2407-514…

NM_001377434.1:c.2407-5142G>T

N/A Intron Variant
USP33 transcript variant 9 NM_001377435.1:c.2110-160…

NM_001377435.1:c.2110-1602G>T

N/A Intron Variant
USP33 transcript variant 10 NM_001377436.1:c.2383-514…

NM_001377436.1:c.2383-5142G>T

N/A Intron Variant
USP33 transcript variant 11 NM_001377437.1:c.2086-160…

NM_001377437.1:c.2086-1602G>T

N/A Intron Variant
USP33 transcript variant 12 NM_001377438.1:c.1963-160…

NM_001377438.1:c.1963-1602G>T

N/A Intron Variant
USP33 transcript variant 13 NM_001377439.1:c.1963-160…

NM_001377439.1:c.1963-1602G>T

N/A Intron Variant
USP33 transcript variant 1 NM_015017.5:c.2500-1602G>T N/A Intron Variant
USP33 transcript variant 2 NM_201624.3:c.2407-1602G>T N/A Intron Variant
USP33 transcript variant 3 NM_201626.3:c. N/A Genic Downstream Transcript Variant
USP33 transcript variant X11 XM_017000729.1:c.2203-514…

XM_017000729.1:c.2203-5142G>T

N/A Intron Variant
USP33 transcript variant X12 XM_011541056.2:c. N/A Genic Downstream Transcript 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 148798 C=0.936511 A=0.063489, T=0.000000
European Sub 127650 C=0.932166 A=0.067834, T=0.000000
African Sub 7040 C=0.9912 A=0.0088, T=0.0000
African Others Sub 242 C=1.000 A=0.000, T=0.000
African American Sub 6798 C=0.9909 A=0.0091, T=0.0000
Asian Sub 604 C=0.901 A=0.099, T=0.000
East Asian Sub 484 C=0.901 A=0.099, T=0.000
Other Asian Sub 120 C=0.900 A=0.100, T=0.000
Latin American 1 Sub 734 C=0.967 A=0.033, T=0.000
Latin American 2 Sub 6266 C=0.9595 A=0.0405, T=0.0000
South Asian Sub 168 C=0.958 A=0.042, T=0.000
Other Sub 6336 C=0.9399 A=0.0601, T=0.0000


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
8.3KJPN JAPANESE Study-wide 16760 C=0.87667 A=0.12333
1000Genomes Global Study-wide 5008 C=0.9427 A=0.0573
1000Genomes African Sub 1322 C=0.9985 A=0.0015
1000Genomes East Asian Sub 1008 C=0.8780 A=0.1220
1000Genomes Europe Sub 1006 C=0.9294 A=0.0706
1000Genomes South Asian Sub 978 C=0.931 A=0.069
1000Genomes American Sub 694 C=0.965 A=0.035
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9176 A=0.0824
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9403 A=0.0597
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9382 A=0.0618
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.8768 A=0.1232
HapMap Global Study-wide 1310 C=0.9260 A=0.0740
HapMap American Sub 768 C=0.943 A=0.057
HapMap Asian Sub 254 C=0.843 A=0.157
HapMap Europe Sub 176 C=0.926 A=0.074
HapMap African Sub 112 C=1.000 A=0.000
Genome-wide autozygosity in Daghestan Global Study-wide 1136 C=0.9261 A=0.0739
Genome-wide autozygosity in Daghestan Daghestan Sub 628 C=0.933 A=0.067
Genome-wide autozygosity in Daghestan Near_East Sub 144 C=0.931 A=0.069
Genome-wide autozygosity in Daghestan Central Asia Sub 122 C=0.869 A=0.131
Genome-wide autozygosity in Daghestan Europe Sub 108 C=0.944 A=0.056
Genome-wide autozygosity in Daghestan South Asian Sub 98 C=0.92 A=0.08
Genome-wide autozygosity in Daghestan Caucasus Sub 36 C=0.94 A=0.06
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.935 A=0.065
Northern Sweden ACPOP Study-wide 600 C=0.945 A=0.055
Qatari Global Study-wide 216 C=0.968 A=0.032
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.902 A=0.098
SGDP_PRJ Global Study-wide 98 C=0.48 A=0.52
The Danish reference pan genome Danish Study-wide 40 C=0.97 A=0.03
Siberian Global Study-wide 12 C=0.50 A=0.50
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 C= A T
GRCh38.p13 chr 1 NC_000001.11:g.77703073= NC_000001.11:g.77703073C>A NC_000001.11:g.77703073C>T
GRCh37.p13 chr 1 NC_000001.10:g.78168758= NC_000001.10:g.78168758C>A NC_000001.10:g.78168758C>T
USP33 transcript variant 4 NM_001377430.1:c.2476-1602= NM_001377430.1:c.2476-1602G>T NM_001377430.1:c.2476-1602G>A
USP33 transcript variant 5 NM_001377431.1:c.2383-1602= NM_001377431.1:c.2383-1602G>T NM_001377431.1:c.2383-1602G>A
USP33 transcript variant 6 NM_001377432.1:c.2500-5142= NM_001377432.1:c.2500-5142G>T NM_001377432.1:c.2500-5142G>A
USP33 transcript variant 7 NM_001377433.1:c.2203-1602= NM_001377433.1:c.2203-1602G>T NM_001377433.1:c.2203-1602G>A
USP33 transcript variant 8 NM_001377434.1:c.2407-5142= NM_001377434.1:c.2407-5142G>T NM_001377434.1:c.2407-5142G>A
USP33 transcript variant 9 NM_001377435.1:c.2110-1602= NM_001377435.1:c.2110-1602G>T NM_001377435.1:c.2110-1602G>A
USP33 transcript variant 10 NM_001377436.1:c.2383-5142= NM_001377436.1:c.2383-5142G>T NM_001377436.1:c.2383-5142G>A
USP33 transcript variant 11 NM_001377437.1:c.2086-1602= NM_001377437.1:c.2086-1602G>T NM_001377437.1:c.2086-1602G>A
USP33 transcript variant 12 NM_001377438.1:c.1963-1602= NM_001377438.1:c.1963-1602G>T NM_001377438.1:c.1963-1602G>A
USP33 transcript variant 13 NM_001377439.1:c.1963-1602= NM_001377439.1:c.1963-1602G>T NM_001377439.1:c.1963-1602G>A
USP33 transcript variant 1 NM_015017.4:c.2500-1602= NM_015017.4:c.2500-1602G>T NM_015017.4:c.2500-1602G>A
USP33 transcript variant 1 NM_015017.5:c.2500-1602= NM_015017.5:c.2500-1602G>T NM_015017.5:c.2500-1602G>A
USP33 transcript variant 2 NM_201624.2:c.2407-1602= NM_201624.2:c.2407-1602G>T NM_201624.2:c.2407-1602G>A
USP33 transcript variant 2 NM_201624.3:c.2407-1602= NM_201624.3:c.2407-1602G>T NM_201624.3:c.2407-1602G>A
USP33 transcript variant X1 XM_005270647.1:c.2500-1602= XM_005270647.1:c.2500-1602G>T XM_005270647.1:c.2500-1602G>A
USP33 transcript variant X1 XM_005270648.1:c.2476-1602= XM_005270648.1:c.2476-1602G>T XM_005270648.1:c.2476-1602G>A
USP33 transcript variant X3 XM_005270649.1:c.2500-5142= XM_005270649.1:c.2500-5142G>T XM_005270649.1:c.2500-5142G>A
USP33 transcript variant X11 XM_017000729.1:c.2203-5142= XM_017000729.1:c.2203-5142G>T XM_017000729.1:c.2203-5142G>A
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#.

73 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18069703 Feb 28, 2004 (120)
2 ILLUMINA ss75092861 Dec 06, 2007 (129)
3 KRIBB_YJKIM ss119742136 Dec 01, 2009 (131)
4 ILLUMINA ss160026515 Dec 01, 2009 (131)
5 COMPLETE_GENOMICS ss166726183 Jul 04, 2010 (132)
6 ILLUMINA ss171794642 Jul 04, 2010 (132)
7 1000GENOMES ss230596445 Jul 14, 2010 (132)
8 1000GENOMES ss238277574 Jul 15, 2010 (132)
9 GMI ss275886893 May 04, 2012 (137)
10 ILLUMINA ss479653149 May 04, 2012 (137)
11 ILLUMINA ss479658455 May 04, 2012 (137)
12 ILLUMINA ss480171899 Sep 08, 2015 (146)
13 ILLUMINA ss484625222 May 04, 2012 (137)
14 ILLUMINA ss536747066 Sep 08, 2015 (146)
15 SSMP ss648147315 Apr 25, 2013 (138)
16 ILLUMINA ss778397707 Sep 08, 2015 (146)
17 ILLUMINA ss782759425 Sep 08, 2015 (146)
18 ILLUMINA ss783725896 Sep 08, 2015 (146)
19 ILLUMINA ss832011660 Sep 08, 2015 (146)
20 ILLUMINA ss833852840 Sep 08, 2015 (146)
21 EVA-GONL ss975322760 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1068011490 Aug 21, 2014 (142)
23 1000GENOMES ss1291513874 Aug 21, 2014 (142)
24 HAMMER_LAB ss1397250529 Sep 08, 2015 (146)
25 EVA_GENOME_DK ss1574166606 Apr 01, 2015 (144)
26 EVA_DECODE ss1584695746 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1600501138 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1643495171 Apr 01, 2015 (144)
29 EVA_SVP ss1712345485 Apr 01, 2015 (144)
30 ILLUMINA ss1751933579 Sep 08, 2015 (146)
31 WEILL_CORNELL_DGM ss1918526701 Feb 12, 2016 (147)
32 GENOMED ss1966784669 Jul 19, 2016 (147)
33 JJLAB ss2019783708 Sep 14, 2016 (149)
34 USC_VALOUEV ss2147799283 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2163808059 Dec 20, 2016 (150)
36 TOPMED ss2326090126 Dec 20, 2016 (150)
37 TOPMED ss2326090127 Dec 20, 2016 (150)
38 SYSTEMSBIOZJU ss2624402710 Nov 08, 2017 (151)
39 ILLUMINA ss2632535112 Nov 08, 2017 (151)
40 GRF ss2697719634 Nov 08, 2017 (151)
41 GNOMAD ss2756924868 Nov 08, 2017 (151)
42 SWEGEN ss2987062159 Nov 08, 2017 (151)
43 ILLUMINA ss3021101437 Nov 08, 2017 (151)
44 BIOINF_KMB_FNS_UNIBA ss3023653867 Nov 08, 2017 (151)
45 TOPMED ss3080731987 Nov 08, 2017 (151)
46 CSHL ss3343525033 Nov 08, 2017 (151)
47 ILLUMINA ss3626132129 Oct 11, 2018 (152)
48 ILLUMINA ss3630570241 Oct 11, 2018 (152)
49 ILLUMINA ss3632897361 Oct 11, 2018 (152)
50 ILLUMINA ss3633592158 Oct 11, 2018 (152)
51 ILLUMINA ss3634331922 Oct 11, 2018 (152)
52 ILLUMINA ss3635285898 Oct 11, 2018 (152)
53 ILLUMINA ss3636008866 Oct 11, 2018 (152)
54 ILLUMINA ss3637036338 Oct 11, 2018 (152)
55 ILLUMINA ss3637766279 Oct 11, 2018 (152)
56 ILLUMINA ss3640039283 Oct 11, 2018 (152)
57 ILLUMINA ss3642777325 Oct 11, 2018 (152)
58 ILLUMINA ss3651429679 Oct 11, 2018 (152)
59 EGCUT_WGS ss3655140102 Jul 12, 2019 (153)
60 EVA_DECODE ss3687074934 Jul 12, 2019 (153)
61 ILLUMINA ss3725037067 Jul 12, 2019 (153)
62 ACPOP ss3727181876 Jul 12, 2019 (153)
63 ILLUMINA ss3744632897 Jul 12, 2019 (153)
64 EVA ss3746392745 Jul 12, 2019 (153)
65 ILLUMINA ss3772134199 Jul 12, 2019 (153)
66 KHV_HUMAN_GENOMES ss3799398479 Jul 12, 2019 (153)
67 EVA ss3826250753 Apr 25, 2020 (154)
68 SGDP_PRJ ss3849169027 Apr 25, 2020 (154)
69 KRGDB ss3894213024 Apr 25, 2020 (154)
70 EVA ss4016919155 Apr 25, 2021 (155)
71 TOPMED ss4455321031 Apr 25, 2021 (155)
72 TOPMED ss4455321032 Apr 25, 2021 (155)
73 TOMMO_GENOMICS ss5144640749 Apr 25, 2021 (155)
74 1000Genomes NC_000001.10 - 78168758 Oct 11, 2018 (152)
75 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 78168758 Oct 11, 2018 (152)
76 Genome-wide autozygosity in Daghestan NC_000001.9 - 77941346 Apr 25, 2020 (154)
77 Genetic variation in the Estonian population NC_000001.10 - 78168758 Oct 11, 2018 (152)
78 The Danish reference pan genome NC_000001.10 - 78168758 Apr 25, 2020 (154)
79 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 15935391 (NC_000001.11:77703072:C:A 8246/140086)
Row 15935392 (NC_000001.11:77703072:C:T 1/140102)

- Apr 25, 2021 (155)
80 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 15935391 (NC_000001.11:77703072:C:A 8246/140086)
Row 15935392 (NC_000001.11:77703072:C:T 1/140102)

- Apr 25, 2021 (155)
81 Genome of the Netherlands Release 5 NC_000001.10 - 78168758 Apr 25, 2020 (154)
82 HapMap NC_000001.11 - 77703073 Apr 25, 2020 (154)
83 KOREAN population from KRGDB NC_000001.10 - 78168758 Apr 25, 2020 (154)
84 Northern Sweden NC_000001.10 - 78168758 Jul 12, 2019 (153)
85 Qatari NC_000001.10 - 78168758 Apr 25, 2020 (154)
86 SGDP_PRJ NC_000001.10 - 78168758 Apr 25, 2020 (154)
87 Siberian NC_000001.10 - 78168758 Apr 25, 2020 (154)
88 8.3KJPN NC_000001.10 - 78168758 Apr 25, 2021 (155)
89 TopMed

Submission ignored due to conflicting rows:
Row 18927366 (NC_000001.11:77703072:C:A 13800/264690)
Row 18927367 (NC_000001.11:77703072:C:T 1/264690)

- Apr 25, 2021 (155)
90 TopMed

Submission ignored due to conflicting rows:
Row 18927366 (NC_000001.11:77703072:C:A 13800/264690)
Row 18927367 (NC_000001.11:77703072:C:T 1/264690)

- Apr 25, 2021 (155)
91 UK 10K study - Twins NC_000001.10 - 78168758 Oct 11, 2018 (152)
92 A Vietnamese Genetic Variation Database NC_000001.10 - 78168758 Jul 12, 2019 (153)
93 ALFA NC_000001.11 - 77703073 Apr 25, 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
11883, ss166726183, ss275886893, ss479653149, ss1397250529, ss1584695746, ss1712345485, ss3642777325 NC_000001.9:77941345:C:A NC_000001.11:77703072:C:A (self)
2254937, 1236125, 878350, 1566112, 530591, 1390418, 466741, 568631, 1186007, 315637, 2610056, 1236125, 262005, ss230596445, ss238277574, ss479658455, ss480171899, ss484625222, ss536747066, ss648147315, ss778397707, ss782759425, ss783725896, ss832011660, ss833852840, ss975322760, ss1068011490, ss1291513874, ss1574166606, ss1600501138, ss1643495171, ss1751933579, ss1918526701, ss1966784669, ss2019783708, ss2147799283, ss2326090126, ss2624402710, ss2632535112, ss2697719634, ss2756924868, ss2987062159, ss3021101437, ss3343525033, ss3626132129, ss3630570241, ss3632897361, ss3633592158, ss3634331922, ss3635285898, ss3636008866, ss3637036338, ss3637766279, ss3640039283, ss3651429679, ss3655140102, ss3727181876, ss3744632897, ss3746392745, ss3772134199, ss3826250753, ss3849169027, ss3894213024, ss4016919155, ss5144640749 NC_000001.10:78168757:C:A NC_000001.11:77703072:C:A (self)
104040, 11921122, 4114299690, ss2163808059, ss3023653867, ss3080731987, ss3687074934, ss3725037067, ss3799398479, ss4455321031 NC_000001.11:77703072:C:A NC_000001.11:77703072:C:A (self)
ss18069703 NT_026943.13:2988931:C:A NC_000001.11:77703072:C:A (self)
ss75092861, ss119742136, ss160026515, ss171794642 NT_032977.9:48140675:C:A NC_000001.11:77703072:C:A (self)
ss2326090127 NC_000001.10:78168757:C:T NC_000001.11:77703072:C:T (self)
4114299690, ss4455321032 NC_000001.11:77703072:C:T NC_000001.11:77703072:C:T
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 rs12021502

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.post596+ae089ad