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.

rs9424288

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3821175 (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
A>C / A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.333794 (88352/264690, TOPMED)
A=0.333312 (46695/140094, GnomAD)
A=0.37417 (7068/18890, ALFA) (+ 14 more)
A=0.43711 (7326/16760, 8.3KJPN)
A=0.3097 (1551/5008, 1000G)
A=0.4219 (1890/4480, Estonian)
A=0.4388 (1691/3854, ALSPAC)
A=0.4415 (1637/3708, TWINSUK)
A=0.3433 (1006/2930, KOREAN)
A=0.417 (416/998, GoNL)
A=0.442 (265/600, NorthernSweden)
A=0.227 (109/480, SGDP_PRJ)
A=0.278 (89/320, HapMap)
A=0.255 (55/216, Qatari)
A=0.290 (62/214, Vietnamese)
A=0.24 (12/50, Siberian)
A=0.35 (14/40, GENOME_DK)
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.3821175A>C
GRCh38.p13 chr 1 NC_000001.11:g.3821175A>G
GRCh37.p13 chr 1 NC_000001.10:g.3737739A>C
GRCh37.p13 chr 1 NC_000001.10:g.3737739A>G
CEP104 RefSeqGene NG_046726.1:g.41059T>G
CEP104 RefSeqGene NG_046726.1:g.41059T>C
Gene: CEP104, centrosomal protein 104 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CEP104 transcript NM_014704.4:c.2571+1999T>G N/A Intron Variant
CEP104 transcript variant X2 XM_005244815.4:c.2679+199…

XM_005244815.4:c.2679+1999T>G

N/A Intron Variant
CEP104 transcript variant X3 XM_011542474.3:c.2589+199…

XM_011542474.3:c.2589+1999T>G

N/A Intron Variant
CEP104 transcript variant X7 XM_017002918.2:c.2397+199…

XM_017002918.2:c.2397+1999T>G

N/A Intron Variant
CEP104 transcript variant X8 XM_017002919.2:c.2373+199…

XM_017002919.2:c.2373+1999T>G

N/A Intron Variant
CEP104 transcript variant X1 XM_024451101.1:c.2697+199…

XM_024451101.1:c.2697+1999T>G

N/A Intron Variant
CEP104 transcript variant X4 XM_024451102.1:c.2523+199…

XM_024451102.1:c.2523+1999T>G

N/A Intron Variant
CEP104 transcript variant X5 XM_024451103.1:c.2505+199…

XM_024451103.1:c.2505+1999T>G

N/A Intron Variant
CEP104 transcript variant X6 XM_024451104.1:c.2499+199…

XM_024451104.1:c.2499+1999T>G

N/A Intron Variant
CEP104 transcript variant X9 XM_024451106.1:c.2325+199…

XM_024451106.1:c.2325+1999T>G

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 18890 A=0.37417 C=0.62583
European Sub 14286 A=0.42650 C=0.57350
African Sub 2946 A=0.1283 C=0.8717
African Others Sub 114 A=0.053 C=0.947
African American Sub 2832 A=0.1314 C=0.8686
Asian Sub 112 A=0.339 C=0.661
East Asian Sub 86 A=0.29 C=0.71
Other Asian Sub 26 A=0.50 C=0.50
Latin American 1 Sub 146 A=0.301 C=0.699
Latin American 2 Sub 610 A=0.407 C=0.593
South Asian Sub 98 A=0.24 C=0.76
Other Sub 692 A=0.351 C=0.649


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 A=0.333794 C=0.666206
gnomAD - Genomes Global Study-wide 140094 A=0.333312 C=0.666688
gnomAD - Genomes European Sub 75868 A=0.41918 C=0.58082
gnomAD - Genomes African Sub 41992 A=0.13853 C=0.86147
gnomAD - Genomes American Sub 13632 A=0.45173 C=0.54827
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.3472 C=0.6528
gnomAD - Genomes East Asian Sub 3128 A=0.3197 C=0.6803
gnomAD - Genomes Other Sub 2150 A=0.3553 C=0.6447
8.3KJPN JAPANESE Study-wide 16760 A=0.43711 C=0.56289
1000Genomes Global Study-wide 5008 A=0.3097 C=0.6903
1000Genomes African Sub 1322 A=0.0847 C=0.9153
1000Genomes East Asian Sub 1008 A=0.3383 C=0.6617
1000Genomes Europe Sub 1006 A=0.4294 C=0.5706
1000Genomes South Asian Sub 978 A=0.332 C=0.668
1000Genomes American Sub 694 A=0.491 C=0.509
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.4219 C=0.5781
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.4388 C=0.5612
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.4415 C=0.5585
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.3433 C=0.6567, G=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.417 C=0.583
Northern Sweden ACPOP Study-wide 600 A=0.442 C=0.558
SGDP_PRJ Global Study-wide 480 A=0.227 C=0.773
HapMap Global Study-wide 320 A=0.278 C=0.722
HapMap African Sub 116 A=0.026 C=0.974
HapMap American Sub 114 A=0.439 C=0.561
HapMap Asian Sub 90 A=0.40 C=0.60
Qatari Global Study-wide 216 A=0.255 C=0.745
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.290 C=0.710
Siberian Global Study-wide 50 A=0.24 C=0.76
The Danish reference pan genome Danish Study-wide 40 A=0.35 C=0.65
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 A= C G
GRCh38.p13 chr 1 NC_000001.11:g.3821175= NC_000001.11:g.3821175A>C NC_000001.11:g.3821175A>G
GRCh37.p13 chr 1 NC_000001.10:g.3737739= NC_000001.10:g.3737739A>C NC_000001.10:g.3737739A>G
CEP104 RefSeqGene NG_046726.1:g.41059= NG_046726.1:g.41059T>G NG_046726.1:g.41059T>C
CEP104 transcript NM_014704.3:c.2571+1999= NM_014704.3:c.2571+1999T>G NM_014704.3:c.2571+1999T>C
CEP104 transcript NM_014704.4:c.2571+1999= NM_014704.4:c.2571+1999T>G NM_014704.4:c.2571+1999T>C
CEP104 transcript variant X1 XM_005244815.1:c.2679+1999= XM_005244815.1:c.2679+1999T>G XM_005244815.1:c.2679+1999T>C
CEP104 transcript variant X2 XM_005244815.4:c.2679+1999= XM_005244815.4:c.2679+1999T>G XM_005244815.4:c.2679+1999T>C
CEP104 transcript variant X3 XM_011542474.3:c.2589+1999= XM_011542474.3:c.2589+1999T>G XM_011542474.3:c.2589+1999T>C
CEP104 transcript variant X7 XM_017002918.2:c.2397+1999= XM_017002918.2:c.2397+1999T>G XM_017002918.2:c.2397+1999T>C
CEP104 transcript variant X8 XM_017002919.2:c.2373+1999= XM_017002919.2:c.2373+1999T>G XM_017002919.2:c.2373+1999T>C
CEP104 transcript variant X1 XM_024451101.1:c.2697+1999= XM_024451101.1:c.2697+1999T>G XM_024451101.1:c.2697+1999T>C
CEP104 transcript variant X4 XM_024451102.1:c.2523+1999= XM_024451102.1:c.2523+1999T>G XM_024451102.1:c.2523+1999T>C
CEP104 transcript variant X5 XM_024451103.1:c.2505+1999= XM_024451103.1:c.2505+1999T>G XM_024451103.1:c.2505+1999T>C
CEP104 transcript variant X6 XM_024451104.1:c.2499+1999= XM_024451104.1:c.2499+1999T>G XM_024451104.1:c.2499+1999T>C
CEP104 transcript variant X9 XM_024451106.1:c.2325+1999= XM_024451106.1:c.2325+1999T>G XM_024451106.1:c.2325+1999T>C
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#.

64 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss12992579 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss16419195 Feb 27, 2004 (120)
3 SSAHASNP ss20574231 Apr 05, 2004 (121)
4 ABI ss41217177 Mar 14, 2006 (126)
5 HGSV ss77565925 Dec 06, 2007 (129)
6 HGSV ss85667026 Dec 16, 2007 (130)
7 BCMHGSC_JDW ss87174444 Mar 23, 2008 (129)
8 HUMANGENOME_JCVI ss97915497 Feb 06, 2009 (130)
9 BGI ss105114947 Dec 01, 2009 (131)
10 1000GENOMES ss107949073 Jan 22, 2009 (130)
11 1000GENOMES ss109967568 Jan 24, 2009 (130)
12 ILLUMINA-UK ss118453555 Feb 14, 2009 (130)
13 ENSEMBL ss138971434 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss163004935 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss163738273 Jul 04, 2010 (132)
16 BUSHMAN ss197925145 Jul 04, 2010 (132)
17 BCM-HGSC-SUB ss205344357 Jul 04, 2010 (132)
18 1000GENOMES ss218203293 Jul 14, 2010 (132)
19 1000GENOMES ss230404181 Jul 14, 2010 (132)
20 1000GENOMES ss238123059 Jul 15, 2010 (132)
21 BL ss252880463 May 09, 2011 (134)
22 GMI ss275691479 May 04, 2012 (137)
23 GMI ss283991025 Apr 25, 2013 (138)
24 PJP ss290498334 May 09, 2011 (134)
25 TISHKOFF ss553734729 Apr 25, 2013 (138)
26 SSMP ss647536528 Apr 25, 2013 (138)
27 EVA-GONL ss974796542 Aug 21, 2014 (142)
28 JMKIDD_LAB ss1067627354 Aug 21, 2014 (142)
29 1000GENOMES ss1289451970 Aug 21, 2014 (142)
30 DDI ss1425693037 Apr 01, 2015 (144)
31 EVA_GENOME_DK ss1573860169 Apr 01, 2015 (144)
32 EVA_DECODE ss1584155313 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1599427520 Apr 01, 2015 (144)
34 EVA_UK10K_TWINSUK ss1642421553 Apr 01, 2015 (144)
35 HAMMER_LAB ss1793785169 Sep 08, 2015 (146)
36 WEILL_CORNELL_DGM ss1917992069 Feb 12, 2016 (147)
37 GENOMED ss1966671398 Jul 19, 2016 (147)
38 JJLAB ss2019512189 Sep 14, 2016 (149)
39 USC_VALOUEV ss2147502565 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2159575241 Dec 20, 2016 (150)
41 TOPMED ss2321730177 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2624271857 Nov 08, 2017 (151)
43 GRF ss2697396607 Nov 08, 2017 (151)
44 GNOMAD ss2750973121 Nov 08, 2017 (151)
45 SWEGEN ss2986201442 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3023519717 Nov 08, 2017 (151)
47 TOPMED ss3067128243 Nov 08, 2017 (151)
48 CSHL ss3343288989 Nov 08, 2017 (151)
49 URBANLAB ss3646586775 Oct 11, 2018 (152)
50 EGCUT_WGS ss3654302676 Jul 12, 2019 (153)
51 EVA_DECODE ss3686047352 Jul 12, 2019 (153)
52 ACPOP ss3726740113 Jul 12, 2019 (153)
53 EVA ss3745755440 Jul 12, 2019 (153)
54 PACBIO ss3783308807 Jul 12, 2019 (153)
55 PACBIO ss3788985688 Jul 12, 2019 (153)
56 PACBIO ss3793858318 Jul 12, 2019 (153)
57 KHV_HUMAN_GENOMES ss3798777102 Jul 12, 2019 (153)
58 EVA ss3825994006 Apr 25, 2020 (154)
59 EVA ss3836384185 Apr 25, 2020 (154)
60 EVA ss3841788350 Apr 25, 2020 (154)
61 SGDP_PRJ ss3848069670 Apr 25, 2020 (154)
62 KRGDB ss3892931272 Apr 25, 2020 (154)
63 TOPMED ss4437307734 Apr 25, 2021 (155)
64 TOMMO_GENOMICS ss5142202006 Apr 25, 2021 (155)
65 1000Genomes NC_000001.10 - 3737739 Oct 11, 2018 (152)
66 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3737739 Oct 11, 2018 (152)
67 Genetic variation in the Estonian population NC_000001.10 - 3737739 Oct 11, 2018 (152)
68 The Danish reference pan genome NC_000001.10 - 3737739 Apr 25, 2020 (154)
69 gnomAD - Genomes NC_000001.11 - 3821175 Apr 25, 2021 (155)
70 Genome of the Netherlands Release 5 NC_000001.10 - 3737739 Apr 25, 2020 (154)
71 HapMap NC_000001.11 - 3821175 Apr 25, 2020 (154)
72 KOREAN population from KRGDB NC_000001.10 - 3737739 Apr 25, 2020 (154)
73 Northern Sweden NC_000001.10 - 3737739 Jul 12, 2019 (153)
74 Qatari NC_000001.10 - 3737739 Apr 25, 2020 (154)
75 SGDP_PRJ NC_000001.10 - 3737739 Apr 25, 2020 (154)
76 Siberian NC_000001.10 - 3737739 Apr 25, 2020 (154)
77 8.3KJPN NC_000001.10 - 3737739 Apr 25, 2021 (155)
78 TopMed NC_000001.11 - 3821175 Apr 25, 2021 (155)
79 UK 10K study - Twins NC_000001.10 - 3737739 Oct 11, 2018 (152)
80 A Vietnamese Genetic Variation Database NC_000001.10 - 3737739 Jul 12, 2019 (153)
81 ALFA NC_000001.11 - 3821175 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)
rs61469376 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77565925, ss85667026 NC_000001.8:3760895:A:C NC_000001.11:3821174:A:C (self)
ss87174444, ss107949073, ss109967568, ss118453555, ss163004935, ss163738273, ss197925145, ss205344357, ss252880463, ss275691479, ss283991025, ss290498334, ss1584155313 NC_000001.9:3727598:A:C NC_000001.11:3821174:A:C (self)
120002, 53768, 40924, 1367403, 23148, 108666, 24978, 33999, 86650, 18919, 171313, 53768, 11374, ss218203293, ss230404181, ss238123059, ss553734729, ss647536528, ss974796542, ss1067627354, ss1289451970, ss1425693037, ss1573860169, ss1599427520, ss1642421553, ss1793785169, ss1917992069, ss1966671398, ss2019512189, ss2147502565, ss2321730177, ss2624271857, ss2697396607, ss2750973121, ss2986201442, ss3343288989, ss3654302676, ss3726740113, ss3745755440, ss3783308807, ss3788985688, ss3793858318, ss3825994006, ss3836384185, ss3848069670, ss3892931272, ss5142202006 NC_000001.10:3737738:A:C NC_000001.11:3821174:A:C (self)
865425, 2817, 569093, 914069, 13475949722, ss2159575241, ss3023519717, ss3067128243, ss3646586775, ss3686047352, ss3798777102, ss3841788350, ss4437307734 NC_000001.11:3821174:A:C NC_000001.11:3821174:A:C (self)
ss12992579, ss16419195, ss20574231 NT_004321.15:1044512:A:C NC_000001.11:3821174:A:C (self)
ss41217177, ss97915497, ss105114947, ss138971434 NT_004350.19:3216370:A:C NC_000001.11:3821174:A:C (self)
108666, ss3892931272 NC_000001.10:3737738:A:G NC_000001.11:3821174:A:G (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 rs9424288

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