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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.

rs9424287

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3820529 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.00162 (40/24616, GnomAD)
C=0.00168 (28/16678, 8.3KJPN)
C=0.28739 (4693/16330, ALFA) (+ 8 more)
C=0.0009 (4/4478, Estonian)
C=0.3713 (1088/2930, KOREAN)
C=0.040 (40/998, GoNL)
T=0.500 (200/400, SGDP_PRJ)
C=0.500 (200/400, SGDP_PRJ)
C=0.440 (95/216, Qatari)
T=0.50 (20/40, Siberian)
C=0.50 (20/40, 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.3820529T>C
GRCh37.p13 chr 1 NC_000001.10:g.3737093T>C
CEP104 RefSeqGene NG_046726.1:g.41705A>G
Gene: CEP104, centrosomal protein 104 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CEP104 transcript NM_014704.4:c.2571+2645A>G N/A Intron Variant
CEP104 transcript variant X2 XM_005244815.4:c.2679+264…

XM_005244815.4:c.2679+2645A>G

N/A Intron Variant
CEP104 transcript variant X3 XM_011542474.3:c.2589+264…

XM_011542474.3:c.2589+2645A>G

N/A Intron Variant
CEP104 transcript variant X7 XM_017002918.2:c.2397+264…

XM_017002918.2:c.2397+2645A>G

N/A Intron Variant
CEP104 transcript variant X8 XM_017002919.2:c.2373+264…

XM_017002919.2:c.2373+2645A>G

N/A Intron Variant
CEP104 transcript variant X1 XM_024451101.1:c.2697+264…

XM_024451101.1:c.2697+2645A>G

N/A Intron Variant
CEP104 transcript variant X4 XM_024451102.1:c.2523+264…

XM_024451102.1:c.2523+2645A>G

N/A Intron Variant
CEP104 transcript variant X5 XM_024451103.1:c.2505+264…

XM_024451103.1:c.2505+2645A>G

N/A Intron Variant
CEP104 transcript variant X6 XM_024451104.1:c.2499+264…

XM_024451104.1:c.2499+2645A>G

N/A Intron Variant
CEP104 transcript variant X9 XM_024451106.1:c.2325+264…

XM_024451106.1:c.2325+2645A>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 16330 T=0.71261 C=0.28739
European Sub 12078 T=0.76842 C=0.23158
African Sub 2816 T=0.5195 C=0.4805
African Others Sub 108 T=0.500 C=0.500
African American Sub 2708 T=0.5203 C=0.4797
Asian Sub 108 T=0.648 C=0.352
East Asian Sub 84 T=0.64 C=0.36
Other Asian Sub 24 T=0.67 C=0.33
Latin American 1 Sub 146 T=0.596 C=0.404
Latin American 2 Sub 610 T=0.648 C=0.352
South Asian Sub 94 T=0.55 C=0.45
Other Sub 478 T=0.605 C=0.395


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
gnomAD - Genomes Global Study-wide 24616 T=0.99838 C=0.00162
gnomAD - Genomes European Sub 17186 T=0.99872 C=0.00128
gnomAD - Genomes American Sub 3808 T=0.9987 C=0.0013
gnomAD - Genomes African Sub 2038 T=0.9961 C=0.0039
gnomAD - Genomes East Asian Sub 640 T=0.995 C=0.005
gnomAD - Genomes Ashkenazi Jewish Sub 518 T=0.998 C=0.002
gnomAD - Genomes Other Sub 426 T=0.998 C=0.002
8.3KJPN JAPANESE Study-wide 16678 T=0.99832 C=0.00168
Genetic variation in the Estonian population Estonian Study-wide 4478 T=0.9991 C=0.0009
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.6287 C=0.3713
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.960 C=0.040
SGDP_PRJ Global Study-wide 400 T=0.500 C=0.500
Qatari Global Study-wide 216 T=0.560 C=0.440
Siberian Global Study-wide 40 T=0.50 C=0.50
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 T= C
GRCh38.p13 chr 1 NC_000001.11:g.3820529= NC_000001.11:g.3820529T>C
GRCh37.p13 chr 1 NC_000001.10:g.3737093= NC_000001.10:g.3737093T>C
CEP104 RefSeqGene NG_046726.1:g.41705= NG_046726.1:g.41705A>G
CEP104 transcript NM_014704.3:c.2571+2645= NM_014704.3:c.2571+2645A>G
CEP104 transcript NM_014704.4:c.2571+2645= NM_014704.4:c.2571+2645A>G
CEP104 transcript variant X1 XM_005244815.1:c.2679+2645= XM_005244815.1:c.2679+2645A>G
CEP104 transcript variant X2 XM_005244815.4:c.2679+2645= XM_005244815.4:c.2679+2645A>G
CEP104 transcript variant X3 XM_011542474.3:c.2589+2645= XM_011542474.3:c.2589+2645A>G
CEP104 transcript variant X7 XM_017002918.2:c.2397+2645= XM_017002918.2:c.2397+2645A>G
CEP104 transcript variant X8 XM_017002919.2:c.2373+2645= XM_017002919.2:c.2373+2645A>G
CEP104 transcript variant X1 XM_024451101.1:c.2697+2645= XM_024451101.1:c.2697+2645A>G
CEP104 transcript variant X4 XM_024451102.1:c.2523+2645= XM_024451102.1:c.2523+2645A>G
CEP104 transcript variant X5 XM_024451103.1:c.2505+2645= XM_024451103.1:c.2505+2645A>G
CEP104 transcript variant X6 XM_024451104.1:c.2499+2645= XM_024451104.1:c.2499+2645A>G
CEP104 transcript variant X9 XM_024451106.1:c.2325+2645= XM_024451106.1:c.2325+2645A>G
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#.

32 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss12992578 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss16418774 Feb 27, 2004 (120)
3 SSAHASNP ss20570377 Apr 05, 2004 (121)
4 BGI ss102715124 Dec 01, 2009 (131)
5 ILLUMINA-UK ss118453546 Feb 14, 2009 (130)
6 ENSEMBL ss143654309 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss163004915 Jul 04, 2010 (132)
8 COMPLETE_GENOMICS ss163738231 Jul 04, 2010 (132)
9 BUSHMAN ss197925130 Jul 04, 2010 (132)
10 BCM-HGSC-SUB ss205410980 Jul 04, 2010 (132)
11 1000GENOMES ss210454992 Jul 14, 2010 (132)
12 BL ss252880451 May 09, 2011 (134)
13 GMI ss275691475 May 04, 2012 (137)
14 SSMP ss647536523 Apr 25, 2013 (138)
15 EVA-GONL ss974796532 Aug 21, 2014 (142)
16 HAMMER_LAB ss1793785162 Sep 08, 2015 (146)
17 WEILL_CORNELL_DGM ss1917992061 Feb 12, 2016 (147)
18 ILLUMINA ss1958234778 Feb 12, 2016 (147)
19 USC_VALOUEV ss2147502561 Dec 20, 2016 (150)
20 HUMAN_LONGEVITY ss2159575195 Dec 20, 2016 (150)
21 SYSTEMSBIOZJU ss2624271854 Nov 08, 2017 (151)
22 GRF ss2697396598 Nov 08, 2017 (151)
23 GNOMAD ss2750973065 Nov 08, 2017 (151)
24 ILLUMINA ss3021047659 Nov 08, 2017 (151)
25 BIOINF_KMB_FNS_UNIBA ss3023519714 Nov 08, 2017 (151)
26 TOPMED ss3067128139 Nov 08, 2017 (151)
27 CSHL ss3343288983 Nov 08, 2017 (151)
28 ILLUMINA ss3651370310 Oct 11, 2018 (152)
29 EGCUT_WGS ss3654302664 Jul 12, 2019 (153)
30 SGDP_PRJ ss3848069657 Apr 25, 2020 (154)
31 KRGDB ss3892931258 Apr 25, 2020 (154)
32 TOMMO_GENOMICS ss5142201984 Apr 25, 2021 (155)
33 Genetic variation in the Estonian population NC_000001.10 - 3737093 Oct 11, 2018 (152)
34 gnomAD - Genomes NC_000001.11 - 3820529 Apr 25, 2021 (155)
35 Genome of the Netherlands Release 5 NC_000001.10 - 3737093 Apr 25, 2020 (154)
36 KOREAN population from KRGDB NC_000001.10 - 3737093 Apr 25, 2020 (154)
37 Qatari NC_000001.10 - 3737093 Apr 25, 2020 (154)
38 SGDP_PRJ NC_000001.10 - 3737093 Apr 25, 2020 (154)
39 Siberian NC_000001.10 - 3737093 Apr 25, 2020 (154)
40 8.3KJPN NC_000001.10 - 3737093 Apr 25, 2021 (155)
41 ALFA NC_000001.11 - 3820529 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
ss118453546, ss163004915, ss163738231, ss197925130, ss205410980, ss210454992, ss252880451, ss275691475 NC_000001.9:3726952:T:C NC_000001.11:3820528:T:C (self)
40912, 23138, 108652, 33991, 86637, 18915, 171291, ss647536523, ss974796532, ss1793785162, ss1917992061, ss1958234778, ss2147502561, ss2624271854, ss2697396598, ss2750973065, ss3021047659, ss3343288983, ss3651370310, ss3654302664, ss3848069657, ss3892931258, ss5142201984 NC_000001.10:3737092:T:C NC_000001.11:3820528:T:C (self)
865303, 8621897377, ss2159575195, ss3023519714, ss3067128139 NC_000001.11:3820528:T:C NC_000001.11:3820528:T:C (self)
ss12992578, ss16418774, ss20570377 NT_004321.15:1043866:T:C NC_000001.11:3820528:T:C (self)
ss102715124, ss143654309 NT_004350.19:3215724:T:C NC_000001.11:3820528:T:C (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 rs9424287

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