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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.

rs9424290

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3825445 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.094492 (25011/264690, TOPMED)
T=0.076246 (10684/140126, GnomAD)
T=0.064729 (8980/138732, ALFA) (+ 16 more)
C=0.48496 (8128/16760, 8.3KJPN)
T=0.2218 (1111/5008, 1000G)
T=0.0786 (352/4480, Estonian)
T=0.0537 (207/3854, ALSPAC)
T=0.0442 (164/3708, TWINSUK)
C=0.3840 (1125/2930, KOREAN)
T=0.1131 (128/1132, Daghestan)
T=0.045 (45/998, GoNL)
T=0.070 (42/600, NorthernSweden)
T=0.198 (64/324, HapMap)
C=0.336 (78/232, SGDP_PRJ)
T=0.097 (21/216, Qatari)
C=0.374 (80/214, Vietnamese)
T=0.06 (4/72, Ancient Sardinia)
T=0.12 (5/40, GENOME_DK)
C=0.44 (14/32, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CEP104 : 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.3825445C>T
GRCh37.p13 chr 1 NC_000001.10:g.3742009C>T
CEP104 RefSeqGene NG_046726.1:g.36789G>A
Gene: CEP104, centrosomal protein 104 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CEP104 transcript NM_014704.4:c.2364+313G>A N/A Intron Variant
CEP104 transcript variant X2 XM_005244815.4:c.2472+313…

XM_005244815.4:c.2472+313G>A

N/A Intron Variant
CEP104 transcript variant X3 XM_011542474.3:c.2382+313…

XM_011542474.3:c.2382+313G>A

N/A Intron Variant
CEP104 transcript variant X7 XM_017002918.2:c.2190+313…

XM_017002918.2:c.2190+313G>A

N/A Intron Variant
CEP104 transcript variant X8 XM_017002919.2:c.2166+313…

XM_017002919.2:c.2166+313G>A

N/A Intron Variant
CEP104 transcript variant X1 XM_024451101.1:c.2490+313…

XM_024451101.1:c.2490+313G>A

N/A Intron Variant
CEP104 transcript variant X4 XM_024451102.1:c.2316+313…

XM_024451102.1:c.2316+313G>A

N/A Intron Variant
CEP104 transcript variant X5 XM_024451103.1:c.2298+313…

XM_024451103.1:c.2298+313G>A

N/A Intron Variant
CEP104 transcript variant X6 XM_024451104.1:c.2292+313…

XM_024451104.1:c.2292+313G>A

N/A Intron Variant
CEP104 transcript variant X9 XM_024451106.1:c.2118+313…

XM_024451106.1:c.2118+313G>A

N/A Intron Variant
CEP104 transcript variant X10 XM_024451108.1: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 138732 C=0.935271 T=0.064729
European Sub 119306 C=0.950480 T=0.049520
African Sub 5532 C=0.9568 T=0.0432
African Others Sub 208 C=0.981 T=0.019
African American Sub 5324 C=0.9559 T=0.0441
Asian Sub 622 C=0.397 T=0.603
East Asian Sub 490 C=0.392 T=0.608
Other Asian Sub 132 C=0.417 T=0.583
Latin American 1 Sub 738 C=0.921 T=0.079
Latin American 2 Sub 6230 C=0.7212 T=0.2788
South Asian Sub 184 C=0.652 T=0.348
Other Sub 6120 C=0.9021 T=0.0979


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 C=0.905508 T=0.094492
gnomAD - Genomes Global Study-wide 140126 C=0.923754 T=0.076246
gnomAD - Genomes European Sub 75896 C=0.94052 T=0.05948
gnomAD - Genomes African Sub 42006 C=0.95653 T=0.04347
gnomAD - Genomes American Sub 13626 C=0.85117 T=0.14883
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.9639 T=0.0361
gnomAD - Genomes East Asian Sub 3122 C=0.3687 T=0.6313
gnomAD - Genomes Other Sub 2154 C=0.8955 T=0.1045
8.3KJPN JAPANESE Study-wide 16760 C=0.48496 T=0.51504
1000Genomes Global Study-wide 5008 C=0.7782 T=0.2218
1000Genomes African Sub 1322 C=0.9675 T=0.0325
1000Genomes East Asian Sub 1008 C=0.3929 T=0.6071
1000Genomes Europe Sub 1006 C=0.9404 T=0.0596
1000Genomes South Asian Sub 978 C=0.707 T=0.293
1000Genomes American Sub 694 C=0.843 T=0.157
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9214 T=0.0786
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9463 T=0.0537
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9558 T=0.0442
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.3840 T=0.6160
Genome-wide autozygosity in Daghestan Global Study-wide 1132 C=0.8869 T=0.1131
Genome-wide autozygosity in Daghestan Daghestan Sub 626 C=0.935 T=0.065
Genome-wide autozygosity in Daghestan Near_East Sub 144 C=0.854 T=0.146
Genome-wide autozygosity in Daghestan Central Asia Sub 122 C=0.721 T=0.279
Genome-wide autozygosity in Daghestan Europe Sub 108 C=0.954 T=0.046
Genome-wide autozygosity in Daghestan South Asian Sub 96 C=0.72 T=0.28
Genome-wide autozygosity in Daghestan Caucasus Sub 36 C=1.00 T=0.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.955 T=0.045
Northern Sweden ACPOP Study-wide 600 C=0.930 T=0.070
HapMap Global Study-wide 324 C=0.802 T=0.198
HapMap African Sub 120 C=0.975 T=0.025
HapMap American Sub 114 C=0.921 T=0.079
HapMap Asian Sub 90 C=0.42 T=0.58
SGDP_PRJ Global Study-wide 232 C=0.336 T=0.664
Qatari Global Study-wide 216 C=0.903 T=0.097
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.374 T=0.626
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 72 C=0.94 T=0.06
The Danish reference pan genome Danish Study-wide 40 C=0.88 T=0.12
Siberian Global Study-wide 32 C=0.44 T=0.56
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= T
GRCh38.p13 chr 1 NC_000001.11:g.3825445= NC_000001.11:g.3825445C>T
GRCh37.p13 chr 1 NC_000001.10:g.3742009= NC_000001.10:g.3742009C>T
CEP104 RefSeqGene NG_046726.1:g.36789= NG_046726.1:g.36789G>A
CEP104 transcript NM_014704.3:c.2364+313= NM_014704.3:c.2364+313G>A
CEP104 transcript NM_014704.4:c.2364+313= NM_014704.4:c.2364+313G>A
CEP104 transcript variant X1 XM_005244815.1:c.2472+313= XM_005244815.1:c.2472+313G>A
CEP104 transcript variant X2 XM_005244815.4:c.2472+313= XM_005244815.4:c.2472+313G>A
CEP104 transcript variant X3 XM_011542474.3:c.2382+313= XM_011542474.3:c.2382+313G>A
CEP104 transcript variant X7 XM_017002918.2:c.2190+313= XM_017002918.2:c.2190+313G>A
CEP104 transcript variant X8 XM_017002919.2:c.2166+313= XM_017002919.2:c.2166+313G>A
CEP104 transcript variant X1 XM_024451101.1:c.2490+313= XM_024451101.1:c.2490+313G>A
CEP104 transcript variant X4 XM_024451102.1:c.2316+313= XM_024451102.1:c.2316+313G>A
CEP104 transcript variant X5 XM_024451103.1:c.2298+313= XM_024451103.1:c.2298+313G>A
CEP104 transcript variant X6 XM_024451104.1:c.2292+313= XM_024451104.1:c.2292+313G>A
CEP104 transcript variant X9 XM_024451106.1:c.2118+313= XM_024451106.1:c.2118+313G>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#.

69 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss12992583 Dec 05, 2003 (119)
2 PERLEGEN ss68756691 May 17, 2007 (127)
3 BGI ss105114961 Dec 01, 2009 (131)
4 ILLUMINA ss160986542 Dec 01, 2009 (131)
5 BCM-HGSC-SUB ss205184305 Jul 04, 2010 (132)
6 1000GENOMES ss218203328 Jul 14, 2010 (132)
7 1000GENOMES ss230404207 Jul 14, 2010 (132)
8 1000GENOMES ss238123086 Jul 15, 2010 (132)
9 GMI ss275691501 May 04, 2012 (137)
10 GMI ss283991035 Apr 25, 2013 (138)
11 ILLUMINA ss481897499 May 04, 2012 (137)
12 ILLUMINA ss481930612 May 04, 2012 (137)
13 ILLUMINA ss482888116 Sep 08, 2015 (146)
14 ILLUMINA ss485742755 May 04, 2012 (137)
15 ILLUMINA ss537597638 Sep 08, 2015 (146)
16 TISHKOFF ss553734758 Apr 25, 2013 (138)
17 SSMP ss647536570 Apr 25, 2013 (138)
18 ILLUMINA ss778638790 Sep 08, 2015 (146)
19 ILLUMINA ss783317153 Sep 08, 2015 (146)
20 ILLUMINA ss784269146 Sep 08, 2015 (146)
21 ILLUMINA ss832578692 Sep 08, 2015 (146)
22 ILLUMINA ss834096470 Sep 08, 2015 (146)
23 EVA-GONL ss974796597 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1067627392 Aug 21, 2014 (142)
25 1000GENOMES ss1289452131 Aug 21, 2014 (142)
26 HAMMER_LAB ss1397238568 Sep 08, 2015 (146)
27 EVA_GENOME_DK ss1573860193 Apr 01, 2015 (144)
28 EVA_DECODE ss1584155360 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1599427621 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1642421654 Apr 01, 2015 (144)
31 ILLUMINA ss1751917919 Sep 08, 2015 (146)
32 WEILL_CORNELL_DGM ss1917992128 Feb 12, 2016 (147)
33 GENOMED ss1966671411 Jul 19, 2016 (147)
34 JJLAB ss2019512227 Sep 14, 2016 (149)
35 USC_VALOUEV ss2147502594 Dec 20, 2016 (150)
36 HUMAN_LONGEVITY ss2159575545 Dec 20, 2016 (150)
37 TOPMED ss2321730442 Dec 20, 2016 (150)
38 SYSTEMSBIOZJU ss2624271880 Nov 08, 2017 (151)
39 ILLUMINA ss2632468702 Nov 08, 2017 (151)
40 GRF ss2697396643 Nov 08, 2017 (151)
41 GNOMAD ss2750973498 Nov 08, 2017 (151)
42 SWEGEN ss2986201524 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3023519731 Nov 08, 2017 (151)
44 TOPMED ss3067129132 Nov 08, 2017 (151)
45 CSHL ss3343289024 Nov 08, 2017 (151)
46 ILLUMINA ss3626011949 Oct 11, 2018 (152)
47 ILLUMINA ss3630508005 Oct 11, 2018 (152)
48 ILLUMINA ss3632878563 Oct 11, 2018 (152)
49 ILLUMINA ss3633572196 Oct 11, 2018 (152)
50 ILLUMINA ss3634303498 Oct 11, 2018 (152)
51 ILLUMINA ss3635266374 Oct 11, 2018 (152)
52 ILLUMINA ss3635979788 Oct 11, 2018 (152)
53 ILLUMINA ss3637016726 Oct 11, 2018 (152)
54 ILLUMINA ss3640010863 Oct 11, 2018 (152)
55 ILLUMINA ss3640973636 Oct 11, 2018 (152)
56 ILLUMINA ss3641267450 Oct 11, 2018 (152)
57 EGCUT_WGS ss3654302731 Jul 12, 2019 (153)
58 EVA_DECODE ss3686047441 Jul 12, 2019 (153)
59 ACPOP ss3726740166 Jul 12, 2019 (153)
60 ILLUMINA ss3744604494 Jul 12, 2019 (153)
61 EVA ss3745755516 Jul 12, 2019 (153)
62 ILLUMINA ss3772106149 Jul 12, 2019 (153)
63 KHV_HUMAN_GENOMES ss3798777165 Jul 12, 2019 (153)
64 SGDP_PRJ ss3848069764 Apr 25, 2020 (154)
65 KRGDB ss3892931418 Apr 25, 2020 (154)
66 EVA ss3984774948 Apr 25, 2021 (155)
67 EVA ss4016890114 Apr 25, 2021 (155)
68 TOPMED ss4437308847 Apr 25, 2021 (155)
69 TOMMO_GENOMICS ss5142202196 Apr 25, 2021 (155)
70 1000Genomes NC_000001.10 - 3742009 Oct 11, 2018 (152)
71 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3742009 Oct 11, 2018 (152)
72 Genome-wide autozygosity in Daghestan NC_000001.9 - 3731869 Apr 25, 2020 (154)
73 Genetic variation in the Estonian population NC_000001.10 - 3742009 Oct 11, 2018 (152)
74 The Danish reference pan genome NC_000001.10 - 3742009 Apr 25, 2020 (154)
75 gnomAD - Genomes NC_000001.11 - 3825445 Apr 25, 2021 (155)
76 Genome of the Netherlands Release 5 NC_000001.10 - 3742009 Apr 25, 2020 (154)
77 HapMap NC_000001.11 - 3825445 Apr 25, 2020 (154)
78 KOREAN population from KRGDB NC_000001.10 - 3742009 Apr 25, 2020 (154)
79 Northern Sweden NC_000001.10 - 3742009 Jul 12, 2019 (153)
80 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 3742009 Apr 25, 2021 (155)
81 Qatari NC_000001.10 - 3742009 Apr 25, 2020 (154)
82 SGDP_PRJ NC_000001.10 - 3742009 Apr 25, 2020 (154)
83 Siberian NC_000001.10 - 3742009 Apr 25, 2020 (154)
84 8.3KJPN NC_000001.10 - 3742009 Apr 25, 2021 (155)
85 TopMed NC_000001.11 - 3825445 Apr 25, 2021 (155)
86 UK 10K study - Twins NC_000001.10 - 3742009 Oct 11, 2018 (152)
87 A Vietnamese Genetic Variation Database NC_000001.10 - 3742009 Jul 12, 2019 (153)
88 ALFA NC_000001.11 - 3825445 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
55, ss205184305, ss275691501, ss283991035, ss481897499, ss1397238568, ss1584155360 NC_000001.9:3731868:C:T NC_000001.11:3825444:C:T (self)
120164, 53877, 40979, 1367427, 23200, 108812, 25031, 875, 34058, 86744, 18948, 171503, 53877, 11399, ss218203328, ss230404207, ss238123086, ss481930612, ss482888116, ss485742755, ss537597638, ss553734758, ss647536570, ss778638790, ss783317153, ss784269146, ss832578692, ss834096470, ss974796597, ss1067627392, ss1289452131, ss1573860193, ss1599427621, ss1642421654, ss1751917919, ss1917992128, ss1966671411, ss2019512227, ss2147502594, ss2321730442, ss2624271880, ss2632468702, ss2697396643, ss2750973498, ss2986201524, ss3343289024, ss3626011949, ss3630508005, ss3632878563, ss3633572196, ss3634303498, ss3635266374, ss3635979788, ss3637016726, ss3640010863, ss3640973636, ss3641267450, ss3654302731, ss3726740166, ss3744604494, ss3745755516, ss3772106149, ss3848069764, ss3892931418, ss3984774948, ss4016890114, ss5142202196 NC_000001.10:3742008:C:T NC_000001.11:3825444:C:T (self)
866365, 2831, 569807, 915182, 11825388357, ss2159575545, ss3023519731, ss3067129132, ss3686047441, ss3798777165, ss4437308847 NC_000001.11:3825444:C:T NC_000001.11:3825444:C:T (self)
ss12992583 NT_004321.15:1048782:C:T NC_000001.11:3825444:C:T (self)
ss68756691, ss105114961, ss160986542 NT_004350.19:3220640:C:T NC_000001.11:3825444:C: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 rs9424290

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