Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs2030162

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr2:168225524 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.368053 (97420/264690, TOPMED)
A=0.457008 (115229/252138, ALFA)
A=0.387357 (54192/139902, GnomAD) (+ 19 more)
A=0.27877 (21940/78702, PAGE_STUDY)
A=0.13132 (2201/16760, 8.3KJPN)
A=0.2841 (1423/5008, 1000G)
A=0.4493 (2013/4480, Estonian)
A=0.4922 (1897/3854, ALSPAC)
A=0.4941 (1832/3708, TWINSUK)
A=0.1242 (363/2922, KOREAN)
A=0.2643 (500/1892, HapMap)
A=0.1321 (242/1832, Korea1K)
A=0.490 (489/998, GoNL)
A=0.134 (106/790, PRJEB37584)
A=0.259 (162/626, Chileans)
A=0.438 (263/600, NorthernSweden)
G=0.375 (102/272, SGDP_PRJ)
A=0.319 (69/216, Qatari)
A=0.126 (27/214, Vietnamese)
G=0.35 (22/62, Ancient Sardinia)
A=0.45 (18/40, GENOME_DK)
G=0.38 (15/40, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
STK39 : 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 2 NC_000002.12:g.168225524G>A
GRCh37.p13 chr 2 NC_000002.11:g.169082034G>A
STK39 RefSeqGene NG_052783.1:g.27072C>T
Gene: STK39, serine/threonine kinase 39 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
STK39 transcript NM_013233.3:c.208+21704C>T N/A Intron Variant
STK39 transcript variant X2 XM_005246465.2:c.208+2170…

XM_005246465.2:c.208+21704C>T

N/A Intron Variant
STK39 transcript variant X1 XM_017003813.2:c.208+2170…

XM_017003813.2:c.208+21704C>T

N/A Intron Variant
STK39 transcript variant X3 XM_017003814.2:c.208+2170…

XM_017003814.2:c.208+21704C>T

N/A Intron Variant
STK39 transcript variant X5 XM_017003816.2:c.208+2170…

XM_017003816.2:c.208+21704C>T

N/A Intron Variant
STK39 transcript variant X4 XM_017003815.2:c. N/A Genic Upstream Transcript Variant
STK39 transcript variant X6 XM_017003817.2:c. N/A Genic Upstream 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 252138 G=0.542992 A=0.457008
European Sub 221260 G=0.519520 A=0.480480
African Sub 7502 G=0.7362 A=0.2638
African Others Sub 274 G=0.796 A=0.204
African American Sub 7228 G=0.7340 A=0.2660
Asian Sub 3906 G=0.8548 A=0.1452
East Asian Sub 3142 G=0.8635 A=0.1365
Other Asian Sub 764 G=0.819 A=0.181
Latin American 1 Sub 1174 G=0.6278 A=0.3722
Latin American 2 Sub 8748 G=0.7454 A=0.2546
South Asian Sub 378 G=0.574 A=0.426
Other Sub 9170 G=0.6132 A=0.3868


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=0.631947 A=0.368053
gnomAD - Genomes Global Study-wide 139902 G=0.612643 A=0.387357
gnomAD - Genomes European Sub 75794 G=0.52757 A=0.47243
gnomAD - Genomes African Sub 41892 G=0.72725 A=0.27275
gnomAD - Genomes American Sub 13624 G=0.68930 A=0.31070
gnomAD - Genomes Ashkenazi Jewish Sub 3316 G=0.5452 A=0.4548
gnomAD - Genomes East Asian Sub 3128 G=0.8696 A=0.1304
gnomAD - Genomes Other Sub 2148 G=0.6229 A=0.3771
The PAGE Study Global Study-wide 78702 G=0.72123 A=0.27877
The PAGE Study AfricanAmerican Sub 32516 G=0.71922 A=0.28078
The PAGE Study Mexican Sub 10810 G=0.74570 A=0.25430
The PAGE Study Asian Sub 8318 G=0.8560 A=0.1440
The PAGE Study PuertoRican Sub 7918 G=0.6582 A=0.3418
The PAGE Study NativeHawaiian Sub 4534 G=0.7329 A=0.2671
The PAGE Study Cuban Sub 4230 G=0.5827 A=0.4173
The PAGE Study Dominican Sub 3828 G=0.6565 A=0.3435
The PAGE Study CentralAmerican Sub 2450 G=0.7600 A=0.2400
The PAGE Study SouthAmerican Sub 1982 G=0.7568 A=0.2432
The PAGE Study NativeAmerican Sub 1260 G=0.6159 A=0.3841
The PAGE Study SouthAsian Sub 856 G=0.636 A=0.364
8.3KJPN JAPANESE Study-wide 16760 G=0.86868 A=0.13132
1000Genomes Global Study-wide 5008 G=0.7159 A=0.2841
1000Genomes African Sub 1322 G=0.7693 A=0.2307
1000Genomes East Asian Sub 1008 G=0.8800 A=0.1200
1000Genomes Europe Sub 1006 G=0.5258 A=0.4742
1000Genomes South Asian Sub 978 G=0.657 A=0.343
1000Genomes American Sub 694 G=0.733 A=0.267
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.5507 A=0.4493
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.5078 A=0.4922
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.5059 A=0.4941
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.8758 A=0.1242
HapMap Global Study-wide 1892 G=0.7357 A=0.2643
HapMap American Sub 770 G=0.694 A=0.306
HapMap African Sub 692 G=0.780 A=0.220
HapMap Asian Sub 254 G=0.858 A=0.142
HapMap Europe Sub 176 G=0.568 A=0.432
Korean Genome Project KOREAN Study-wide 1832 G=0.8679 A=0.1321
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.510 A=0.490
CNV burdens in cranial meningiomas Global Study-wide 790 G=0.866 A=0.134
CNV burdens in cranial meningiomas CRM Sub 790 G=0.866 A=0.134
Chileans Chilean Study-wide 626 G=0.741 A=0.259
Northern Sweden ACPOP Study-wide 600 G=0.562 A=0.438
SGDP_PRJ Global Study-wide 272 G=0.375 A=0.625
Qatari Global Study-wide 216 G=0.681 A=0.319
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.874 A=0.126
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 62 G=0.35 A=0.65
The Danish reference pan genome Danish Study-wide 40 G=0.55 A=0.45
Siberian Global Study-wide 40 G=0.38 A=0.62
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
GRCh38.p13 chr 2 NC_000002.12:g.168225524= NC_000002.12:g.168225524G>A
GRCh37.p13 chr 2 NC_000002.11:g.169082034= NC_000002.11:g.169082034G>A
STK39 RefSeqGene NG_052783.1:g.27072= NG_052783.1:g.27072C>T
STK39 transcript NM_013233.2:c.208+21704= NM_013233.2:c.208+21704C>T
STK39 transcript NM_013233.3:c.208+21704= NM_013233.3:c.208+21704C>T
STK39 transcript variant X1 XM_005246465.1:c.208+21704= XM_005246465.1:c.208+21704C>T
STK39 transcript variant X2 XM_005246465.2:c.208+21704= XM_005246465.2:c.208+21704C>T
STK39 transcript variant X1 XM_017003813.2:c.208+21704= XM_017003813.2:c.208+21704C>T
STK39 transcript variant X3 XM_017003814.2:c.208+21704= XM_017003814.2:c.208+21704C>T
STK39 transcript variant X5 XM_017003816.2:c.208+21704= XM_017003816.2:c.208+21704C>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#.

101 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2938910 Apr 12, 2001 (94)
2 SSAHASNP ss21671333 Apr 05, 2004 (121)
3 AFFY ss66186341 Nov 29, 2006 (127)
4 AFFY ss76257168 Dec 08, 2007 (129)
5 KRIBB_YJKIM ss81662907 Dec 15, 2007 (130)
6 BCMHGSC_JDW ss91431661 Mar 24, 2008 (129)
7 1000GENOMES ss110226530 Jan 24, 2009 (130)
8 1000GENOMES ss111238180 Jan 25, 2009 (130)
9 ILLUMINA ss120244569 Dec 01, 2009 (131)
10 ENSEMBL ss138573329 Dec 01, 2009 (131)
11 ENSEMBL ss139667976 Dec 01, 2009 (131)
12 GMI ss157958141 Dec 01, 2009 (131)
13 ILLUMINA ss160490766 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss164784639 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss165578847 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss167394237 Jul 04, 2010 (132)
17 AFFY ss173002601 Jul 04, 2010 (132)
18 BUSHMAN ss201343701 Jul 04, 2010 (132)
19 1000GENOMES ss219642139 Jul 14, 2010 (132)
20 1000GENOMES ss231459560 Jul 14, 2010 (132)
21 1000GENOMES ss238950034 Jul 15, 2010 (132)
22 ILLUMINA ss244255987 Jul 04, 2010 (132)
23 GMI ss276778001 May 04, 2012 (137)
24 ILLUMINA ss480387888 May 04, 2012 (137)
25 ILLUMINA ss480400740 May 04, 2012 (137)
26 ILLUMINA ss481178481 Sep 08, 2015 (146)
27 ILLUMINA ss484991559 May 04, 2012 (137)
28 ILLUMINA ss537025384 Sep 08, 2015 (146)
29 TISHKOFF ss556021993 Apr 25, 2013 (138)
30 SSMP ss649673249 Apr 25, 2013 (138)
31 ILLUMINA ss778850811 Sep 08, 2015 (146)
32 ILLUMINA ss782942080 Sep 08, 2015 (146)
33 ILLUMINA ss783904640 Sep 08, 2015 (146)
34 ILLUMINA ss832197753 Sep 08, 2015 (146)
35 ILLUMINA ss834311461 Sep 08, 2015 (146)
36 EVA-GONL ss977620179 Aug 21, 2014 (142)
37 JMKIDD_LAB ss1069687675 Aug 21, 2014 (142)
38 1000GENOMES ss1300338882 Aug 21, 2014 (142)
39 DDI ss1428813807 Apr 01, 2015 (144)
40 EVA_GENOME_DK ss1579188494 Apr 01, 2015 (144)
41 EVA_DECODE ss1587057599 Apr 01, 2015 (144)
42 EVA_UK10K_ALSPAC ss1605099423 Apr 01, 2015 (144)
43 EVA_UK10K_TWINSUK ss1648093456 Apr 01, 2015 (144)
44 EVA_SVP ss1712507630 Apr 01, 2015 (144)
45 ILLUMINA ss1752322188 Sep 08, 2015 (146)
46 HAMMER_LAB ss1797881094 Sep 08, 2015 (146)
47 WEILL_CORNELL_DGM ss1920872400 Feb 12, 2016 (147)
48 ILLUMINA ss1946057550 Feb 12, 2016 (147)
49 ILLUMINA ss1958476769 Feb 12, 2016 (147)
50 GENOMED ss1968947429 Jul 19, 2016 (147)
51 JJLAB ss2020970019 Sep 14, 2016 (149)
52 USC_VALOUEV ss2149034850 Dec 20, 2016 (150)
53 HUMAN_LONGEVITY ss2236394493 Dec 20, 2016 (150)
54 TOPMED ss2402806478 Dec 20, 2016 (150)
55 SYSTEMSBIOZJU ss2624989094 Nov 08, 2017 (151)
56 ILLUMINA ss2633701800 Nov 08, 2017 (151)
57 ILLUMINA ss2635096680 Nov 08, 2017 (151)
58 GRF ss2703671912 Nov 08, 2017 (151)
59 ILLUMINA ss2710916560 Nov 08, 2017 (151)
60 GNOMAD ss2782564888 Nov 08, 2017 (151)
61 SWEGEN ss2990827702 Nov 08, 2017 (151)
62 ILLUMINA ss3022038045 Nov 08, 2017 (151)
63 BIOINF_KMB_FNS_UNIBA ss3024245423 Nov 08, 2017 (151)
64 TOPMED ss3329686434 Nov 08, 2017 (151)
65 CSHL ss3344594674 Nov 08, 2017 (151)
66 ILLUMINA ss3625769778 Oct 11, 2018 (152)
67 ILLUMINA ss3628216372 Oct 11, 2018 (152)
68 ILLUMINA ss3631663548 Oct 11, 2018 (152)
69 ILLUMINA ss3633224075 Oct 11, 2018 (152)
70 ILLUMINA ss3633936848 Oct 11, 2018 (152)
71 ILLUMINA ss3634797409 Oct 11, 2018 (152)
72 ILLUMINA ss3635622517 Oct 11, 2018 (152)
73 ILLUMINA ss3636486666 Oct 11, 2018 (152)
74 ILLUMINA ss3637374501 Oct 11, 2018 (152)
75 ILLUMINA ss3640504708 Oct 11, 2018 (152)
76 ILLUMINA ss3641116534 Oct 11, 2018 (152)
77 ILLUMINA ss3641412594 Oct 11, 2018 (152)
78 ILLUMINA ss3644760177 Oct 11, 2018 (152)
79 URBANLAB ss3647200939 Oct 11, 2018 (152)
80 ILLUMINA ss3652482351 Oct 11, 2018 (152)
81 EGCUT_WGS ss3658697642 Jul 13, 2019 (153)
82 EVA_DECODE ss3705378536 Jul 13, 2019 (153)
83 ILLUMINA ss3725843350 Jul 13, 2019 (153)
84 ACPOP ss3729086006 Jul 13, 2019 (153)
85 ILLUMINA ss3744185963 Jul 13, 2019 (153)
86 ILLUMINA ss3745097257 Jul 13, 2019 (153)
87 EVA ss3757692894 Jul 13, 2019 (153)
88 PAGE_CC ss3770963183 Jul 13, 2019 (153)
89 ILLUMINA ss3772593854 Jul 13, 2019 (153)
90 KHV_HUMAN_GENOMES ss3802051414 Jul 13, 2019 (153)
91 EVA ss3827341874 Apr 25, 2020 (154)
92 EVA ss3837088745 Apr 25, 2020 (154)
93 EVA ss3842508526 Apr 25, 2020 (154)
94 SGDP_PRJ ss3853927475 Apr 25, 2020 (154)
95 KRGDB ss3899555840 Apr 25, 2020 (154)
96 KOGIC ss3949455636 Apr 25, 2020 (154)
97 EVA ss3984493210 Apr 26, 2021 (155)
98 EVA ss3984935851 Apr 26, 2021 (155)
99 EVA ss4017032940 Apr 26, 2021 (155)
100 TOPMED ss4532975191 Apr 26, 2021 (155)
101 TOMMO_GENOMICS ss5155015657 Apr 26, 2021 (155)
102 1000Genomes NC_000002.11 - 169082034 Oct 11, 2018 (152)
103 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 169082034 Oct 11, 2018 (152)
104 Chileans NC_000002.11 - 169082034 Apr 25, 2020 (154)
105 Genetic variation in the Estonian population NC_000002.11 - 169082034 Oct 11, 2018 (152)
106 The Danish reference pan genome NC_000002.11 - 169082034 Apr 25, 2020 (154)
107 gnomAD - Genomes NC_000002.12 - 168225524 Apr 26, 2021 (155)
108 Genome of the Netherlands Release 5 NC_000002.11 - 169082034 Apr 25, 2020 (154)
109 HapMap NC_000002.12 - 168225524 Apr 25, 2020 (154)
110 KOREAN population from KRGDB NC_000002.11 - 169082034 Apr 25, 2020 (154)
111 Korean Genome Project NC_000002.12 - 168225524 Apr 25, 2020 (154)
112 Northern Sweden NC_000002.11 - 169082034 Jul 13, 2019 (153)
113 The PAGE Study NC_000002.12 - 168225524 Jul 13, 2019 (153)
114 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000002.11 - 169082034 Apr 26, 2021 (155)
115 CNV burdens in cranial meningiomas NC_000002.11 - 169082034 Apr 26, 2021 (155)
116 Qatari NC_000002.11 - 169082034 Apr 25, 2020 (154)
117 SGDP_PRJ NC_000002.11 - 169082034 Apr 25, 2020 (154)
118 Siberian NC_000002.11 - 169082034 Apr 25, 2020 (154)
119 8.3KJPN NC_000002.11 - 169082034 Apr 26, 2021 (155)
120 TopMed NC_000002.12 - 168225524 Apr 26, 2021 (155)
121 UK 10K study - Twins NC_000002.11 - 169082034 Oct 11, 2018 (152)
122 A Vietnamese Genetic Variation Database NC_000002.11 - 169082034 Jul 13, 2019 (153)
123 ALFA NC_000002.12 - 168225524 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)
rs58323025 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss91431661, ss110226530, ss111238180, ss164784639, ss165578847, ss167394237, ss201343701, ss276778001, ss480387888, ss1587057599, ss1712507630, ss2635096680 NC_000002.10:168790279:G:A NC_000002.12:168225523:G:A (self)
11392799, 6285279, 235473, 4435890, 5353433, 2761198, 6733234, 2370871, 161778, 42545, 2914330, 5944455, 1551204, 12984964, 6285279, 1365787, ss219642139, ss231459560, ss238950034, ss480400740, ss481178481, ss484991559, ss537025384, ss556021993, ss649673249, ss778850811, ss782942080, ss783904640, ss832197753, ss834311461, ss977620179, ss1069687675, ss1300338882, ss1428813807, ss1579188494, ss1605099423, ss1648093456, ss1752322188, ss1797881094, ss1920872400, ss1946057550, ss1958476769, ss1968947429, ss2020970019, ss2149034850, ss2402806478, ss2624989094, ss2633701800, ss2703671912, ss2710916560, ss2782564888, ss2990827702, ss3022038045, ss3344594674, ss3625769778, ss3628216372, ss3631663548, ss3633224075, ss3633936848, ss3634797409, ss3635622517, ss3636486666, ss3637374501, ss3640504708, ss3641116534, ss3641412594, ss3644760177, ss3652482351, ss3658697642, ss3729086006, ss3744185963, ss3745097257, ss3757692894, ss3772593854, ss3827341874, ss3837088745, ss3853927475, ss3899555840, ss3984493210, ss3984935851, ss4017032940, ss5155015657 NC_000002.11:169082033:G:A NC_000002.12:168225523:G:A (self)
81222891, 1944280, 5833637, 184652, 210170629, 336798070, 3749396784, ss2236394493, ss3024245423, ss3329686434, ss3647200939, ss3705378536, ss3725843350, ss3770963183, ss3802051414, ss3842508526, ss3949455636, ss4532975191 NC_000002.12:168225523:G:A NC_000002.12:168225523:G:A (self)
ss21671333 NT_005403.14:19291450:G:A NC_000002.12:168225523:G:A (self)
ss2938910, ss66186341, ss76257168, ss81662907, ss120244569, ss138573329, ss139667976, ss157958141, ss160490766, ss173002601, ss244255987 NT_005403.17:19291451:G:A NC_000002.12:168225523:G:A (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 rs2030162

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