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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.

rs10875289

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:100382413 (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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.247055 (65393/264690, TOPMED)
A=0.10803 (1153/10673, ALFA)
A=0.2310 (1157/5008, 1000G) (+ 8 more)
A=0.2823 (826/2926, KOREAN)
A=0.2848 (520/1826, Korea1K)
A=0.333 (332/998, GoNL)
A=0.323 (185/572, NorthernSweden)
A=0.250 (54/216, Qatari)
G=0.417 (85/204, SGDP_PRJ)
A=0.33 (13/40, GENOME_DK)
G=0.39 (11/28, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CDC14A : 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.100382413G>A
GRCh38.p13 chr 1 NC_000001.11:g.100382413G>T
GRCh37.p13 chr 1 NC_000001.10:g.100847969G>A
GRCh37.p13 chr 1 NC_000001.10:g.100847969G>T
CDC14A RefSeqGene (LRG_1418) NG_051602.2:g.42413G>A
CDC14A RefSeqGene (LRG_1418) NG_051602.2:g.42413G>T
Gene: CDC14A, cell division cycle 14A (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CDC14A transcript variant 4 NM_001319210.2:c.216+4792…

NM_001319210.2:c.216+4792G>A

N/A Intron Variant
CDC14A transcript variant 5 NM_001319211.2:c.42+4792G…

NM_001319211.2:c.42+4792G>A

N/A Intron Variant
CDC14A transcript variant 6 NM_001319212.2:c.-576+479…

NM_001319212.2:c.-576+4792G>A

N/A Intron Variant
CDC14A transcript variant 1 NM_003672.4:c.216+4792G>A N/A Intron Variant
CDC14A transcript variant 2 NM_033312.3:c.216+4792G>A N/A Intron Variant
CDC14A transcript variant 3 NM_033313.3:c.216+4792G>A N/A Intron Variant
CDC14A transcript variant X1 XM_005271294.3:c.219+4792…

XM_005271294.3:c.219+4792G>A

N/A Intron Variant
CDC14A transcript variant X4 XM_005271296.3:c.219+4792…

XM_005271296.3:c.219+4792G>A

N/A Intron Variant
CDC14A transcript variant X3 XM_011542340.2:c.219+4792…

XM_011542340.2:c.219+4792G>A

N/A Intron Variant
CDC14A transcript variant X2 XM_011542341.3:c.180+4792…

XM_011542341.3:c.180+4792G>A

N/A Intron Variant
CDC14A transcript variant X7 XM_017002646.1:c.219+4792…

XM_017002646.1:c.219+4792G>A

N/A Intron Variant
CDC14A transcript variant X8 XM_017002647.1:c.216+4792…

XM_017002647.1:c.216+4792G>A

N/A Intron Variant
CDC14A transcript variant X5 XM_024450503.1:c.42+4792G…

XM_024450503.1:c.42+4792G>A

N/A Intron Variant
CDC14A transcript variant X11 XM_024450504.1:c.-774+479…

XM_024450504.1:c.-774+4792G>A

N/A Intron Variant
CDC14A transcript variant X12 XM_024450505.1:c.-576+479…

XM_024450505.1:c.-576+4792G>A

N/A Intron Variant
CDC14A transcript variant X6 XM_011542345.3:c. N/A Genic Upstream Transcript Variant
CDC14A transcript variant X13 XM_024450506.1:c. N/A Genic Upstream Transcript Variant
CDC14A transcript variant X9 XR_002957887.1:n. N/A Intron Variant
CDC14A transcript variant X10 XR_002957888.1:n. 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
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 10673 G=0.86124 A=0.10803, T=0.03073
European Sub 7491 G=0.8024 A=0.1538, T=0.0438
African Sub 2468 G=1.0000 A=0.0000, T=0.0000
African Others Sub 108 G=1.000 A=0.000, T=0.000
African American Sub 2360 G=1.0000 A=0.0000, T=0.0000
Asian Sub 60 G=1.00 A=0.00, T=0.00
East Asian Sub 54 G=1.00 A=0.00, T=0.00
Other Asian Sub 6 G=1.0 A=0.0, T=0.0
Latin American 1 Sub 72 G=1.00 A=0.00, T=0.00
Latin American 2 Sub 254 G=1.000 A=0.000, T=0.000
South Asian Sub 38 G=1.00 A=0.00, T=0.00
Other Sub 290 G=0.997 A=0.003, T=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=0.752945 A=0.247055
Allele Frequency Aggregator Total Global 10673 G=0.86124 A=0.10803, T=0.03073
Allele Frequency Aggregator European Sub 7491 G=0.8024 A=0.1538, T=0.0438
Allele Frequency Aggregator African Sub 2468 G=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Other Sub 290 G=0.997 A=0.003, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 254 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 72 G=1.00 A=0.00, T=0.00
Allele Frequency Aggregator Asian Sub 60 G=1.00 A=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 38 G=1.00 A=0.00, T=0.00
1000Genomes Global Study-wide 5008 G=0.7690 A=0.2310
1000Genomes African Sub 1322 G=0.9811 A=0.0189
1000Genomes East Asian Sub 1008 G=0.7073 A=0.2927
1000Genomes Europe Sub 1006 G=0.6581 A=0.3419
1000Genomes South Asian Sub 978 G=0.710 A=0.290
1000Genomes American Sub 694 G=0.699 A=0.301
KOREAN population from KRGDB KOREAN Study-wide 2926 G=0.7177 A=0.2823
Korean Genome Project KOREAN Study-wide 1826 G=0.7152 A=0.2848
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.667 A=0.333
Northern Sweden ACPOP Study-wide 572 G=0.677 A=0.323
Qatari Global Study-wide 216 G=0.750 A=0.250
SGDP_PRJ Global Study-wide 204 G=0.417 A=0.583
The Danish reference pan genome Danish Study-wide 40 G=0.68 A=0.33
Siberian Global Study-wide 28 G=0.39 A=0.61
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 T
GRCh38.p13 chr 1 NC_000001.11:g.100382413= NC_000001.11:g.100382413G>A NC_000001.11:g.100382413G>T
GRCh37.p13 chr 1 NC_000001.10:g.100847969= NC_000001.10:g.100847969G>A NC_000001.10:g.100847969G>T
CDC14A RefSeqGene (LRG_1418) NG_051602.2:g.42413= NG_051602.2:g.42413G>A NG_051602.2:g.42413G>T
CDC14A transcript variant 4 NM_001319210.2:c.216+4792= NM_001319210.2:c.216+4792G>A NM_001319210.2:c.216+4792G>T
CDC14A transcript variant 5 NM_001319211.2:c.42+4792= NM_001319211.2:c.42+4792G>A NM_001319211.2:c.42+4792G>T
CDC14A transcript variant 6 NM_001319212.2:c.-576+4792= NM_001319212.2:c.-576+4792G>A NM_001319212.2:c.-576+4792G>T
CDC14A transcript variant 1 NM_003672.3:c.216+4792= NM_003672.3:c.216+4792G>A NM_003672.3:c.216+4792G>T
CDC14A transcript variant 1 NM_003672.4:c.216+4792= NM_003672.4:c.216+4792G>A NM_003672.4:c.216+4792G>T
CDC14A transcript variant 2 NM_033312.2:c.216+4792= NM_033312.2:c.216+4792G>A NM_033312.2:c.216+4792G>T
CDC14A transcript variant 2 NM_033312.3:c.216+4792= NM_033312.3:c.216+4792G>A NM_033312.3:c.216+4792G>T
CDC14A transcript variant 3 NM_033313.2:c.216+4792= NM_033313.2:c.216+4792G>A NM_033313.2:c.216+4792G>T
CDC14A transcript variant 3 NM_033313.3:c.216+4792= NM_033313.3:c.216+4792G>A NM_033313.3:c.216+4792G>T
CDC14A transcript variant X1 XM_005271294.1:c.219+4792= XM_005271294.1:c.219+4792G>A XM_005271294.1:c.219+4792G>T
CDC14A transcript variant X1 XM_005271294.3:c.219+4792= XM_005271294.3:c.219+4792G>A XM_005271294.3:c.219+4792G>T
CDC14A transcript variant X2 XM_005271295.1:c.216+4792= XM_005271295.1:c.216+4792G>A XM_005271295.1:c.216+4792G>T
CDC14A transcript variant X3 XM_005271296.1:c.219+4792= XM_005271296.1:c.219+4792G>A XM_005271296.1:c.219+4792G>T
CDC14A transcript variant X4 XM_005271296.3:c.219+4792= XM_005271296.3:c.219+4792G>A XM_005271296.3:c.219+4792G>T
CDC14A transcript variant X4 XM_005271297.1:c.42+4792= XM_005271297.1:c.42+4792G>A XM_005271297.1:c.42+4792G>T
CDC14A transcript variant X3 XM_011542340.2:c.219+4792= XM_011542340.2:c.219+4792G>A XM_011542340.2:c.219+4792G>T
CDC14A transcript variant X2 XM_011542341.3:c.180+4792= XM_011542341.3:c.180+4792G>A XM_011542341.3:c.180+4792G>T
CDC14A transcript variant X7 XM_017002646.1:c.219+4792= XM_017002646.1:c.219+4792G>A XM_017002646.1:c.219+4792G>T
CDC14A transcript variant X8 XM_017002647.1:c.216+4792= XM_017002647.1:c.216+4792G>A XM_017002647.1:c.216+4792G>T
CDC14A transcript variant X5 XM_024450503.1:c.42+4792= XM_024450503.1:c.42+4792G>A XM_024450503.1:c.42+4792G>T
CDC14A transcript variant X11 XM_024450504.1:c.-774+4792= XM_024450504.1:c.-774+4792G>A XM_024450504.1:c.-774+4792G>T
CDC14A transcript variant X12 XM_024450505.1:c.-576+4792= XM_024450505.1:c.-576+4792G>A XM_024450505.1:c.-576+4792G>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#.

47 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss16384117 Feb 27, 2004 (120)
2 SC_SNP ss18069719 Feb 27, 2004 (120)
3 SC_SNP ss18243022 Feb 27, 2004 (120)
4 SSAHASNP ss20429430 Apr 05, 2004 (121)
5 ABI ss41130445 Mar 14, 2006 (126)
6 ENSEMBL ss161151980 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss164878987 Jul 04, 2010 (132)
8 COMPLETE_GENOMICS ss166908815 Jul 04, 2010 (132)
9 1000GENOMES ss218551595 Jul 14, 2010 (132)
10 1000GENOMES ss230658839 Jul 14, 2010 (132)
11 1000GENOMES ss238325195 Jul 15, 2010 (132)
12 BL ss253319507 May 09, 2011 (134)
13 GMI ss275947019 May 04, 2012 (137)
14 GMI ss284106549 Apr 25, 2013 (138)
15 PJP ss290581489 May 09, 2011 (134)
16 EVA-GONL ss975488984 Aug 21, 2014 (142)
17 1000GENOMES ss1292127818 Aug 21, 2014 (142)
18 DDI ss1425912600 Apr 01, 2015 (144)
19 EVA_GENOME_DK ss1574275071 Apr 01, 2015 (144)
20 EVA_DECODE ss1584866992 Apr 01, 2015 (144)
21 EVA_DECODE ss1584866993 Apr 01, 2015 (144)
22 WEILL_CORNELL_DGM ss1918687960 Feb 12, 2016 (147)
23 JJLAB ss2019865861 Sep 14, 2016 (149)
24 USC_VALOUEV ss2147884368 Dec 20, 2016 (150)
25 SYSTEMSBIOZJU ss2624443898 Nov 08, 2017 (151)
26 GRF ss2697811578 Nov 08, 2017 (151)
27 SWEGEN ss2987314174 Nov 08, 2017 (151)
28 BIOINF_KMB_FNS_UNIBA ss3023696166 Nov 08, 2017 (151)
29 TOPMED ss3084787937 Nov 08, 2017 (151)
30 TOPMED ss3084787938 Nov 08, 2017 (151)
31 EVA_DECODE ss3687377665 Jul 12, 2019 (153)
32 EVA_DECODE ss3687377666 Jul 12, 2019 (153)
33 ACPOP ss3727318929 Jul 12, 2019 (153)
34 EVA ss3746580068 Jul 12, 2019 (153)
35 PACBIO ss3783497593 Jul 12, 2019 (153)
36 PACBIO ss3789142286 Jul 12, 2019 (153)
37 PACBIO ss3794015133 Jul 12, 2019 (153)
38 KHV_HUMAN_GENOMES ss3799580872 Jul 12, 2019 (153)
39 EVA ss3826329485 Apr 25, 2020 (154)
40 SGDP_PRJ ss3849488120 Apr 25, 2020 (154)
41 KRGDB ss3894567450 Apr 25, 2020 (154)
42 KOGIC ss3945101198 Apr 25, 2020 (154)
43 GNOMAD ss3999085854 Apr 25, 2021 (155)
44 GNOMAD ss3999085867 Apr 25, 2021 (155)
45 TOPMED ss4460884888 Apr 25, 2021 (155)
46 TOMMO_GENOMICS ss5145336940 Apr 25, 2021 (155)
47 TOMMO_GENOMICS ss5145336941 Apr 25, 2021 (155)
48 1000Genomes NC_000001.10 - 100847969 Oct 11, 2018 (152)
49 The Danish reference pan genome NC_000001.10 - 100847969 Apr 25, 2020 (154)
50 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 20450087 (NC_000001.11:100382412:G:A 33144/108722)
Row 20450100 (NC_000001.11:100382412:G:T 274/108630)

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

Submission ignored due to conflicting rows:
Row 20450087 (NC_000001.11:100382412:G:A 33144/108722)
Row 20450100 (NC_000001.11:100382412:G:T 274/108630)

- Apr 25, 2021 (155)
52 Genome of the Netherlands Release 5 NC_000001.10 - 100847969 Apr 25, 2020 (154)
53 KOREAN population from KRGDB NC_000001.10 - 100847969 Apr 25, 2020 (154)
54 Korean Genome Project NC_000001.11 - 100382413 Apr 25, 2020 (154)
55 Northern Sweden NC_000001.10 - 100847969 Jul 12, 2019 (153)
56 Qatari NC_000001.10 - 100847969 Apr 25, 2020 (154)
57 SGDP_PRJ NC_000001.10 - 100847969 Apr 25, 2020 (154)
58 Siberian NC_000001.10 - 100847969 Apr 25, 2020 (154)
59 8.3KJPN

Submission ignored due to conflicting rows:
Row 3306247 (NC_000001.10:100847968:G:A 5186/16702)
Row 3306248 (NC_000001.10:100847968:G:T 52/16702)

- Apr 25, 2021 (155)
60 8.3KJPN

Submission ignored due to conflicting rows:
Row 3306247 (NC_000001.10:100847968:G:A 5186/16702)
Row 3306248 (NC_000001.10:100847968:G:T 52/16702)

- Apr 25, 2021 (155)
61 TopMed NC_000001.11 - 100382413 Apr 25, 2021 (155)
62 ALFA NC_000001.11 - 100382413 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).

Associated ID History Updated (Build)
rs116949437 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss164878987, ss166908815, ss253319507, ss275947019, ss284106549, ss290581489, ss1584866992 NC_000001.9:100620556:G:A NC_000001.11:100382412:G:A (self)
2892280, 1630974, 692908, 1744844, 603794, 729890, 1505100, 400722, ss218551595, ss230658839, ss238325195, ss975488984, ss1292127818, ss1425912600, ss1574275071, ss1918687960, ss2019865861, ss2147884368, ss2624443898, ss2697811578, ss2987314174, ss3727318929, ss3746580068, ss3783497593, ss3789142286, ss3794015133, ss3826329485, ss3849488120, ss3894567450, ss5145336940 NC_000001.10:100847968:G:A NC_000001.11:100382412:G:A (self)
1479199, 24491223, 935409009, ss3023696166, ss3084787937, ss3687377665, ss3799580872, ss3945101198, ss3999085854, ss4460884888 NC_000001.11:100382412:G:A NC_000001.11:100382412:G:A (self)
ss16384117, ss18069719, ss18243022, ss20429430 NT_028050.13:9036912:G:A NC_000001.11:100382412:G:A (self)
ss41130445, ss161151980 NT_032977.9:70819886:G:A NC_000001.11:100382412:G:A (self)
ss1584866993 NC_000001.9:100620556:G:T NC_000001.11:100382412:G:T (self)
ss5145336941 NC_000001.10:100847968:G:T NC_000001.11:100382412:G:T (self)
935409009, ss3084787938, ss3687377666, ss3999085867 NC_000001.11:100382412:G:T NC_000001.11:100382412: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 rs10875289

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