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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.

rs1904415

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:60780695 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.276675 (73233/264690, TOPMED)
G=0.250913 (35731/142404, ALFA)
G=0.271851 (38045/139948, GnomAD) (+ 17 more)
G=0.22637 (3794/16760, 8.3KJPN)
G=0.2488 (1246/5008, 1000G)
G=0.2444 (1095/4480, Estonian)
G=0.2639 (1017/3854, ALSPAC)
G=0.2586 (959/3708, TWINSUK)
G=0.1614 (473/2930, KOREAN)
G=0.2277 (474/2082, HGDP_Stanford)
G=0.2850 (538/1888, HapMap)
G=0.1599 (293/1832, Korea1K)
G=0.253 (252/998, GoNL)
G=0.177 (106/600, NorthernSweden)
G=0.171 (85/496, SGDP_PRJ)
G=0.227 (49/216, Qatari)
G=0.110 (23/210, Vietnamese)
G=0.15 (8/54, Siberian)
G=0.33 (13/40, GENOME_DK)
T=0.0 (0/2, Ancient Sardinia)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CDK1 : 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 10 NC_000010.11:g.60780695G>T
GRCh37.p13 chr 10 NC_000010.10:g.62540453G>T
CDK1 RefSeqGene NG_029877.1:g.7365G>T
Gene: CDK1, cyclin dependent kinase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CDK1 transcript variant 4 NM_001170406.1:c.37+493G>T N/A Intron Variant
CDK1 transcript variant 5 NM_001170407.2:c.37+493G>T N/A Intron Variant
CDK1 transcript variant 6 NM_001320918.1:c.37+493G>T N/A Intron Variant
CDK1 transcript variant 1 NM_001786.5:c.37+493G>T N/A Intron Variant
CDK1 transcript variant 2 NM_033379.5:c.37+493G>T N/A Intron Variant
CDK1 transcript variant X1 XM_005270303.3:c.37+493G>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

ALFA Allele Frequency (New)
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 142404 G=0.250913 T=0.749087
European Sub 125792 G=0.246009 T=0.753991
African Sub 6676 G=0.3704 T=0.6296
African Others Sub 242 G=0.384 T=0.616
African American Sub 6434 G=0.3699 T=0.6301
Asian Sub 622 G=0.162 T=0.838
East Asian Sub 492 G=0.161 T=0.839
Other Asian Sub 130 G=0.169 T=0.831
Latin American 1 Sub 690 G=0.259 T=0.741
Latin American 2 Sub 2252 G=0.2087 T=0.7913
South Asian Sub 182 G=0.198 T=0.802
Other Sub 6190 G=0.2465 T=0.7535


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=0.276675 T=0.723325
gnomAD - Genomes Global Study-wide 139948 G=0.271851 T=0.728149
gnomAD - Genomes European Sub 75826 G=0.23166 T=0.76834
gnomAD - Genomes African Sub 41880 G=0.37137 T=0.62863
gnomAD - Genomes American Sub 13636 G=0.23079 T=0.76921
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.2265 T=0.7735
gnomAD - Genomes East Asian Sub 3130 G=0.1511 T=0.8489
gnomAD - Genomes Other Sub 2152 G=0.2570 T=0.7430
8.3KJPN JAPANESE Study-wide 16760 G=0.22637 T=0.77363
1000Genomes Global Study-wide 5008 G=0.2488 T=0.7512
1000Genomes African Sub 1322 G=0.4228 T=0.5772
1000Genomes East Asian Sub 1008 G=0.1538 T=0.8462
1000Genomes Europe Sub 1006 G=0.2018 T=0.7982
1000Genomes South Asian Sub 978 G=0.182 T=0.818
1000Genomes American Sub 694 G=0.218 T=0.782
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.2444 T=0.7556
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.2639 T=0.7361
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.2586 T=0.7414
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.1614 T=0.8386
HGDP-CEPH-db Supplement 1 Global Study-wide 2082 G=0.2277 T=0.7723
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 G=0.136 T=0.864
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.188 T=0.812
HGDP-CEPH-db Supplement 1 Middle_Est Sub 348 G=0.259 T=0.741
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=0.247 T=0.753
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=0.364 T=0.636
HGDP-CEPH-db Supplement 1 America Sub 216 G=0.167 T=0.833
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=0.54 T=0.46
HapMap Global Study-wide 1888 G=0.2850 T=0.7150
HapMap American Sub 770 G=0.264 T=0.736
HapMap African Sub 688 G=0.356 T=0.644
HapMap Asian Sub 254 G=0.193 T=0.807
HapMap Europe Sub 176 G=0.233 T=0.767
Korean Genome Project KOREAN Study-wide 1832 G=0.1599 T=0.8401
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.253 T=0.747
Northern Sweden ACPOP Study-wide 600 G=0.177 T=0.823
SGDP_PRJ Global Study-wide 496 G=0.171 T=0.829
Qatari Global Study-wide 216 G=0.227 T=0.773
A Vietnamese Genetic Variation Database Global Study-wide 210 G=0.110 T=0.890
Siberian Global Study-wide 54 G=0.15 T=0.85
The Danish reference pan genome Danish Study-wide 40 G=0.33 T=0.68
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 2 G=1.0 T=0.0
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= T
GRCh38.p13 chr 10 NC_000010.11:g.60780695= NC_000010.11:g.60780695G>T
GRCh37.p13 chr 10 NC_000010.10:g.62540453= NC_000010.10:g.62540453G>T
CDK1 RefSeqGene NG_029877.1:g.7365= NG_029877.1:g.7365G>T
CDK1 transcript variant 4 NM_001170406.1:c.37+493= NM_001170406.1:c.37+493G>T
CDK1 transcript variant 5 NM_001170407.1:c.37+493= NM_001170407.1:c.37+493G>T
CDK1 transcript variant 5 NM_001170407.2:c.37+493= NM_001170407.2:c.37+493G>T
CDK1 transcript variant 6 NM_001320918.1:c.37+493= NM_001320918.1:c.37+493G>T
CDK1 transcript variant 1 NM_001786.4:c.37+493= NM_001786.4:c.37+493G>T
CDK1 transcript variant 1 NM_001786.5:c.37+493= NM_001786.5:c.37+493G>T
CDK1 transcript variant 2 NM_033379.4:c.37+493= NM_033379.4:c.37+493G>T
CDK1 transcript variant 2 NM_033379.5:c.37+493= NM_033379.5:c.37+493G>T
CDK1 transcript variant X1 XM_005270303.1:c.37+493= XM_005270303.1:c.37+493G>T
CDK1 transcript variant X1 XM_005270303.3:c.37+493= XM_005270303.3:c.37+493G>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#.

104 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2788010 Jan 12, 2001 (92)
2 SC_JCM ss3443667 Sep 28, 2001 (100)
3 EGP_SNPS ss4473531 Jul 03, 2002 (106)
4 SC_JCM ss5677835 Feb 20, 2003 (111)
5 SC_SNP ss12953990 Dec 05, 2003 (119)
6 SC_SNP ss15867152 Feb 27, 2004 (120)
7 CSHL-HAPMAP ss16483375 Feb 27, 2004 (120)
8 CSHL-HAPMAP ss17392915 Feb 27, 2004 (120)
9 SSAHASNP ss20704891 Apr 05, 2004 (121)
10 PERLEGEN ss23532995 Sep 20, 2004 (123)
11 ILLUMINA ss67597849 Nov 30, 2006 (127)
12 ILLUMINA ss71247705 May 17, 2007 (127)
13 ILLUMINA ss75335667 Dec 06, 2007 (129)
14 HGSV ss79030610 Dec 06, 2007 (129)
15 BCMHGSC_JDW ss88235982 Mar 23, 2008 (129)
16 HUMANGENOME_JCVI ss97560252 Feb 04, 2009 (130)
17 BGI ss102883663 Dec 01, 2009 (131)
18 1000GENOMES ss109491056 Jan 24, 2009 (130)
19 1000GENOMES ss113347922 Jan 25, 2009 (130)
20 ILLUMINA-UK ss119190225 Feb 15, 2009 (130)
21 KRIBB_YJKIM ss119407917 Dec 01, 2009 (131)
22 ENSEMBL ss131902952 Dec 01, 2009 (131)
23 ENSEMBL ss137964364 Dec 01, 2009 (131)
24 GMI ss155112506 Dec 01, 2009 (131)
25 ILLUMINA ss160474920 Dec 01, 2009 (131)
26 COMPLETE_GENOMICS ss170176288 Jul 04, 2010 (132)
27 ILLUMINA ss172978548 Jul 04, 2010 (132)
28 BUSHMAN ss201594696 Jul 04, 2010 (132)
29 BCM-HGSC-SUB ss207091302 Jul 04, 2010 (132)
30 1000GENOMES ss224758404 Jul 14, 2010 (132)
31 1000GENOMES ss235199376 Jul 15, 2010 (132)
32 1000GENOMES ss241900606 Jul 15, 2010 (132)
33 BL ss254360710 May 09, 2011 (134)
34 GMI ss280640496 May 04, 2012 (137)
35 GMI ss286201331 Apr 25, 2013 (138)
36 PJP ss290850720 May 09, 2011 (134)
37 ILLUMINA ss480338089 May 04, 2012 (137)
38 ILLUMINA ss480349681 May 04, 2012 (137)
39 ILLUMINA ss481115167 Sep 08, 2015 (146)
40 ILLUMINA ss484966663 May 04, 2012 (137)
41 ILLUMINA ss537006411 Sep 08, 2015 (146)
42 SSMP ss656817961 Apr 25, 2013 (138)
43 ILLUMINA ss778471794 Sep 08, 2015 (146)
44 ILLUMINA ss782929644 Sep 08, 2015 (146)
45 ILLUMINA ss783892470 Sep 08, 2015 (146)
46 ILLUMINA ss832185001 Sep 08, 2015 (146)
47 ILLUMINA ss833927590 Sep 08, 2015 (146)
48 EVA-GONL ss987549925 Aug 21, 2014 (142)
49 JMKIDD_LAB ss1077032361 Aug 21, 2014 (142)
50 1000GENOMES ss1337668147 Aug 21, 2014 (142)
51 DDI ss1426339621 Apr 01, 2015 (144)
52 EVA_GENOME_DK ss1575154348 Apr 01, 2015 (144)
53 EVA_DECODE ss1597216371 Apr 01, 2015 (144)
54 EVA_UK10K_ALSPAC ss1624687058 Apr 01, 2015 (144)
55 EVA_UK10K_TWINSUK ss1667681091 Apr 01, 2015 (144)
56 EVA_SVP ss1713183909 Apr 01, 2015 (144)
57 ILLUMINA ss1751974930 Sep 08, 2015 (146)
58 WEILL_CORNELL_DGM ss1930913850 Feb 12, 2016 (147)
59 GENOMED ss1967143016 Jul 19, 2016 (147)
60 JJLAB ss2026180179 Sep 14, 2016 (149)
61 USC_VALOUEV ss2154453320 Dec 20, 2016 (150)
62 HUMAN_LONGEVITY ss2175218228 Dec 20, 2016 (150)
63 TOPMED ss2338250523 Dec 20, 2016 (150)
64 SYSTEMSBIOZJU ss2627560466 Nov 08, 2017 (151)
65 ILLUMINA ss2632717873 Nov 08, 2017 (151)
66 ILLUMINA ss2635014925 Nov 08, 2017 (151)
67 GRF ss2698697443 Nov 08, 2017 (151)
68 GNOMAD ss2889431097 Nov 08, 2017 (151)
69 SWEGEN ss3006573014 Nov 08, 2017 (151)
70 BIOINF_KMB_FNS_UNIBA ss3026881262 Nov 08, 2017 (151)
71 TOPMED ss3121338315 Nov 08, 2017 (151)
72 CSHL ss3349150370 Nov 08, 2017 (151)
73 ILLUMINA ss3626458026 Oct 12, 2018 (152)
74 ILLUMINA ss3630743310 Oct 12, 2018 (152)
75 ILLUMINA ss3633648622 Oct 12, 2018 (152)
76 ILLUMINA ss3634406037 Oct 12, 2018 (152)
77 ILLUMINA ss3635341089 Oct 12, 2018 (152)
78 ILLUMINA ss3636089633 Oct 12, 2018 (152)
79 ILLUMINA ss3637091762 Oct 12, 2018 (152)
80 ILLUMINA ss3637852968 Oct 12, 2018 (152)
81 ILLUMINA ss3640113379 Oct 12, 2018 (152)
82 ILLUMINA ss3642856278 Oct 12, 2018 (152)
83 URBANLAB ss3649385556 Oct 12, 2018 (152)
84 EGCUT_WGS ss3673985491 Jul 13, 2019 (153)
85 EVA_DECODE ss3689992825 Jul 13, 2019 (153)
86 ACPOP ss3737373132 Jul 13, 2019 (153)
87 ILLUMINA ss3744706908 Jul 13, 2019 (153)
88 EVA ss3748171951 Jul 13, 2019 (153)
89 ILLUMINA ss3772207479 Jul 13, 2019 (153)
90 PACBIO ss3786689039 Jul 13, 2019 (153)
91 PACBIO ss3791867537 Jul 13, 2019 (153)
92 PACBIO ss3796749555 Jul 13, 2019 (153)
93 KHV_HUMAN_GENOMES ss3813547608 Jul 13, 2019 (153)
94 EVA ss3832155636 Apr 26, 2020 (154)
95 EVA ss3839617326 Apr 26, 2020 (154)
96 EVA ss3845089565 Apr 26, 2020 (154)
97 HGDP ss3847387760 Apr 26, 2020 (154)
98 SGDP_PRJ ss3874329827 Apr 26, 2020 (154)
99 KRGDB ss3922399871 Apr 26, 2020 (154)
100 KOGIC ss3967992440 Apr 26, 2020 (154)
101 EVA ss3985478175 Apr 27, 2021 (155)
102 EVA ss4017488398 Apr 27, 2021 (155)
103 TOPMED ss4854407979 Apr 27, 2021 (155)
104 TOMMO_GENOMICS ss5197891639 Apr 27, 2021 (155)
105 1000Genomes NC_000010.10 - 62540453 Oct 12, 2018 (152)
106 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 62540453 Oct 12, 2018 (152)
107 Genetic variation in the Estonian population NC_000010.10 - 62540453 Oct 12, 2018 (152)
108 The Danish reference pan genome NC_000010.10 - 62540453 Apr 26, 2020 (154)
109 gnomAD - Genomes NC_000010.11 - 60780695 Apr 27, 2021 (155)
110 Genome of the Netherlands Release 5 NC_000010.10 - 62540453 Apr 26, 2020 (154)
111 HGDP-CEPH-db Supplement 1 NC_000010.9 - 62210459 Apr 26, 2020 (154)
112 HapMap NC_000010.11 - 60780695 Apr 26, 2020 (154)
113 KOREAN population from KRGDB NC_000010.10 - 62540453 Apr 26, 2020 (154)
114 Korean Genome Project NC_000010.11 - 60780695 Apr 26, 2020 (154)
115 Northern Sweden NC_000010.10 - 62540453 Jul 13, 2019 (153)
116 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000010.10 - 62540453 Apr 27, 2021 (155)
117 Qatari NC_000010.10 - 62540453 Apr 26, 2020 (154)
118 SGDP_PRJ NC_000010.10 - 62540453 Apr 26, 2020 (154)
119 Siberian NC_000010.10 - 62540453 Apr 26, 2020 (154)
120 8.3KJPN NC_000010.10 - 62540453 Apr 27, 2021 (155)
121 TopMed NC_000010.11 - 60780695 Apr 27, 2021 (155)
122 UK 10K study - Twins NC_000010.10 - 62540453 Oct 12, 2018 (152)
123 A Vietnamese Genetic Variation Database NC_000010.10 - 62540453 Jul 13, 2019 (153)
124 ALFA NC_000010.11 - 60780695 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
ss79030610 NC_000010.8:62210458:G:T NC_000010.11:60780694:G:T (self)
65652, ss88235982, ss109491056, ss113347922, ss119190225, ss170176288, ss201594696, ss207091302, ss254360710, ss280640496, ss286201331, ss290850720, ss480338089, ss1597216371, ss1713183909, ss2635014925, ss3642856278, ss3847387760 NC_000010.9:62210458:G:T NC_000010.11:60780694:G:T (self)
50064513, 27786351, 19723739, 2181685, 12392332, 29577265, 10657997, 704102, 12955780, 26346807, 6969674, 55860946, 27786351, 6171239, ss224758404, ss235199376, ss241900606, ss480349681, ss481115167, ss484966663, ss537006411, ss656817961, ss778471794, ss782929644, ss783892470, ss832185001, ss833927590, ss987549925, ss1077032361, ss1337668147, ss1426339621, ss1575154348, ss1624687058, ss1667681091, ss1751974930, ss1930913850, ss1967143016, ss2026180179, ss2154453320, ss2338250523, ss2627560466, ss2632717873, ss2698697443, ss2889431097, ss3006573014, ss3349150370, ss3626458026, ss3630743310, ss3633648622, ss3634406037, ss3635341089, ss3636089633, ss3637091762, ss3637852968, ss3640113379, ss3673985491, ss3737373132, ss3744706908, ss3748171951, ss3772207479, ss3786689039, ss3791867537, ss3796749555, ss3832155636, ss3839617326, ss3874329827, ss3922399871, ss3985478175, ss4017488398, ss5197891639 NC_000010.10:62540452:G:T NC_000010.11:60780694:G:T (self)
353873697, 415735, 24370441, 43953325, 69953634, 4160514420, ss2175218228, ss3026881262, ss3121338315, ss3649385556, ss3689992825, ss3813547608, ss3845089565, ss3967992440, ss4854407979 NC_000010.11:60780694:G:T NC_000010.11:60780694:G:T (self)
ss12953990 NT_008583.15:11091600:G:T NC_000010.11:60780694:G:T (self)
ss15867152, ss16483375, ss17392915, ss20704891 NT_008583.16:11091607:G:T NC_000010.11:60780694:G:T (self)
ss2788010, ss3443667, ss4473531, ss5677835, ss23532995, ss67597849, ss71247705, ss75335667, ss97560252, ss102883663, ss119407917, ss131902952, ss137964364, ss155112506, ss160474920, ss172978548 NT_030059.13:13344916:G:T NC_000010.11:60780694:G:T (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 rs1904415

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