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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.

rs2275828

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3830019 (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>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.371933 (98447/264690, TOPMED)
T=0.385166 (95606/248220, GnomAD_exome)
T=0.369445 (51709/139964, GnomAD) (+ 16 more)
T=0.383295 (46141/120380, ExAC)
T=0.31419 (6500/20688, ALFA)
T=0.43669 (7319/16760, 8.3KJPN)
T=0.37314 (4853/13006, GO-ESP)
T=0.3498 (1752/5008, 1000G)
T=0.4210 (1886/4480, Estonian)
T=0.4411 (1700/3854, ALSPAC)
T=0.4417 (1638/3708, TWINSUK)
T=0.3427 (1004/2930, KOREAN)
T=0.417 (416/998, GoNL)
T=0.442 (265/600, NorthernSweden)
T=0.448 (239/534, MGP)
G=0.363 (111/306, SGDP_PRJ)
T=0.264 (57/216, Qatari)
T=0.35 (14/40, GENOME_DK)
G=0.40 (12/30, 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.3830019G>C
GRCh38.p13 chr 1 NC_000001.11:g.3830019G>T
GRCh37.p13 chr 1 NC_000001.10:g.3746583G>C
GRCh37.p13 chr 1 NC_000001.10:g.3746583G>T
CEP104 RefSeqGene NG_046726.1:g.32215C>G
CEP104 RefSeqGene NG_046726.1:g.32215C>A
Gene: CEP104, centrosomal protein 104 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CEP104 transcript NM_014704.4:c.1837-22C>G N/A Intron Variant
CEP104 transcript variant X2 XM_005244815.4:c.1945-22C…

XM_005244815.4:c.1945-22C>G

N/A Intron Variant
CEP104 transcript variant X3 XM_011542474.3:c.1855-22C…

XM_011542474.3:c.1855-22C>G

N/A Intron Variant
CEP104 transcript variant X7 XM_017002918.2:c.1663-22C…

XM_017002918.2:c.1663-22C>G

N/A Intron Variant
CEP104 transcript variant X8 XM_017002919.2:c.1639-22C…

XM_017002919.2:c.1639-22C>G

N/A Intron Variant
CEP104 transcript variant X1 XM_024451101.1:c.1963-22C…

XM_024451101.1:c.1963-22C>G

N/A Intron Variant
CEP104 transcript variant X4 XM_024451102.1:c.1789-22C…

XM_024451102.1:c.1789-22C>G

N/A Intron Variant
CEP104 transcript variant X5 XM_024451103.1:c.1771-22C…

XM_024451103.1:c.1771-22C>G

N/A Intron Variant
CEP104 transcript variant X6 XM_024451104.1:c.1765-22C…

XM_024451104.1:c.1765-22C>G

N/A Intron Variant
CEP104 transcript variant X9 XM_024451106.1:c.1591-22C…

XM_024451106.1:c.1591-22C>G

N/A Intron Variant
CEP104 transcript variant X10 XM_024451108.1:c.1963-22C…

XM_024451108.1:c.1963-22C>G

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 20688 G=0.68581 C=0.00000, T=0.31419
European Sub 15232 G=0.65336 C=0.00000, T=0.34664
African Sub 2318 G=0.8960 C=0.0000, T=0.1040
African Others Sub 84 G=0.95 C=0.00, T=0.05
African American Sub 2234 G=0.8939 C=0.0000, T=0.1061
Asian Sub 104 G=0.798 C=0.000, T=0.202
East Asian Sub 68 G=0.84 C=0.00, T=0.16
Other Asian Sub 36 G=0.72 C=0.00, T=0.28
Latin American 1 Sub 74 G=1.00 C=0.00, T=0.00
Latin American 2 Sub 208 G=1.000 C=0.000, T=0.000
South Asian Sub 56 G=0.98 C=0.00, T=0.02
Other Sub 2696 G=0.6450 C=0.0000, T=0.3550


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=0.628067 T=0.371933
gnomAD - Exomes Global Study-wide 248220 G=0.614834 T=0.385166
gnomAD - Exomes European Sub 133840 G=0.580626 T=0.419374
gnomAD - Exomes Asian Sub 48554 G=0.68732 T=0.31268
gnomAD - Exomes American Sub 34094 G=0.57180 T=0.42820
gnomAD - Exomes African Sub 15686 G=0.75067 T=0.24933
gnomAD - Exomes Ashkenazi Jewish Sub 9996 G=0.6619 T=0.3381
gnomAD - Exomes Other Sub 6050 G=0.6025 T=0.3975
gnomAD - Genomes Global Study-wide 139964 G=0.630555 T=0.369445
gnomAD - Genomes European Sub 75830 G=0.58030 T=0.41970
gnomAD - Genomes African Sub 41922 G=0.74672 T=0.25328
gnomAD - Genomes American Sub 13616 G=0.53665 T=0.46335
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.6526 T=0.3474
gnomAD - Genomes East Asian Sub 3126 G=0.6814 T=0.3186
gnomAD - Genomes Other Sub 2148 G=0.6248 T=0.3752
ExAC Global Study-wide 120380 G=0.616705 T=0.383295
ExAC Europe Sub 73044 G=0.57897 T=0.42103
ExAC Asian Sub 24984 G=0.68792 T=0.31208
ExAC American Sub 11456 G=0.58598 T=0.41402
ExAC African Sub 9994 G=0.7470 T=0.2530
ExAC Other Sub 902 G=0.646 T=0.354
8.3KJPN JAPANESE Study-wide 16760 G=0.56331 T=0.43669
GO Exome Sequencing Project Global Study-wide 13006 G=0.62686 T=0.37314
GO Exome Sequencing Project European American Sub 8600 G=0.5690 T=0.4310
GO Exome Sequencing Project African American Sub 4406 G=0.7399 T=0.2601
1000Genomes Global Study-wide 5008 G=0.6502 T=0.3498
1000Genomes African Sub 1322 G=0.7640 T=0.2360
1000Genomes East Asian Sub 1008 G=0.6617 T=0.3383
1000Genomes Europe Sub 1006 G=0.5706 T=0.4294
1000Genomes South Asian Sub 978 G=0.668 T=0.332
1000Genomes American Sub 694 G=0.507 T=0.493
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.5790 T=0.4210
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.5589 T=0.4411
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.5583 T=0.4417
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.6573 T=0.3427
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.583 T=0.417
Northern Sweden ACPOP Study-wide 600 G=0.558 T=0.442
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.552 T=0.448
SGDP_PRJ Global Study-wide 306 G=0.363 T=0.637
Qatari Global Study-wide 216 G=0.736 T=0.264
The Danish reference pan genome Danish Study-wide 40 G=0.65 T=0.35
Siberian Global Study-wide 30 G=0.40 T=0.60
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= C T
GRCh38.p13 chr 1 NC_000001.11:g.3830019= NC_000001.11:g.3830019G>C NC_000001.11:g.3830019G>T
GRCh37.p13 chr 1 NC_000001.10:g.3746583= NC_000001.10:g.3746583G>C NC_000001.10:g.3746583G>T
CEP104 RefSeqGene NG_046726.1:g.32215= NG_046726.1:g.32215C>G NG_046726.1:g.32215C>A
CEP104 transcript NM_014704.3:c.1837-22= NM_014704.3:c.1837-22C>G NM_014704.3:c.1837-22C>A
CEP104 transcript NM_014704.4:c.1837-22= NM_014704.4:c.1837-22C>G NM_014704.4:c.1837-22C>A
CEP104 transcript variant X1 XM_005244815.1:c.1945-22= XM_005244815.1:c.1945-22C>G XM_005244815.1:c.1945-22C>A
CEP104 transcript variant X2 XM_005244815.4:c.1945-22= XM_005244815.4:c.1945-22C>G XM_005244815.4:c.1945-22C>A
CEP104 transcript variant X3 XM_011542474.3:c.1855-22= XM_011542474.3:c.1855-22C>G XM_011542474.3:c.1855-22C>A
CEP104 transcript variant X7 XM_017002918.2:c.1663-22= XM_017002918.2:c.1663-22C>G XM_017002918.2:c.1663-22C>A
CEP104 transcript variant X8 XM_017002919.2:c.1639-22= XM_017002919.2:c.1639-22C>G XM_017002919.2:c.1639-22C>A
CEP104 transcript variant X1 XM_024451101.1:c.1963-22= XM_024451101.1:c.1963-22C>G XM_024451101.1:c.1963-22C>A
CEP104 transcript variant X4 XM_024451102.1:c.1789-22= XM_024451102.1:c.1789-22C>G XM_024451102.1:c.1789-22C>A
CEP104 transcript variant X5 XM_024451103.1:c.1771-22= XM_024451103.1:c.1771-22C>G XM_024451103.1:c.1771-22C>A
CEP104 transcript variant X6 XM_024451104.1:c.1765-22= XM_024451104.1:c.1765-22C>G XM_024451104.1:c.1765-22C>A
CEP104 transcript variant X9 XM_024451106.1:c.1591-22= XM_024451106.1:c.1591-22C>G XM_024451106.1:c.1591-22C>A
CEP104 transcript variant X10 XM_024451108.1:c.1963-22= XM_024451108.1:c.1963-22C>G XM_024451108.1:c.1963-22C>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#.

62 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss3212056 Sep 28, 2001 (100)
2 SC_SNP ss12992585 Dec 05, 2003 (119)
3 ABI ss41339252 Mar 14, 2006 (126)
4 HGSV ss82870072 Dec 16, 2007 (130)
5 BCMHGSC_JDW ss87174552 Mar 23, 2008 (129)
6 ILLUMINA-UK ss118453641 Feb 14, 2009 (130)
7 ENSEMBL ss137763664 Dec 01, 2009 (131)
8 GMI ss154559532 Dec 01, 2009 (131)
9 ENSEMBL ss161249439 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss163005145 Jul 04, 2010 (132)
11 COMPLETE_GENOMICS ss166008874 Jul 04, 2010 (132)
12 1000GENOMES ss210455013 Jul 14, 2010 (132)
13 1000GENOMES ss218203372 Jul 14, 2010 (132)
14 1000GENOMES ss230404240 Jul 14, 2010 (132)
15 1000GENOMES ss238123115 Jul 15, 2010 (132)
16 GMI ss275691526 May 04, 2012 (137)
17 GMI ss283991048 Apr 25, 2013 (138)
18 1000GENOMES ss489716761 May 04, 2012 (137)
19 TISHKOFF ss553734800 Apr 25, 2013 (138)
20 SSMP ss647536608 Apr 25, 2013 (138)
21 NHLBI-ESP ss712268032 Apr 25, 2013 (138)
22 EVA-GONL ss974796661 Aug 21, 2014 (142)
23 1000GENOMES ss1289452300 Aug 21, 2014 (142)
24 DDI ss1425693095 Apr 01, 2015 (144)
25 EVA_GENOME_DK ss1573860229 Apr 01, 2015 (144)
26 EVA_DECODE ss1584155412 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1599427714 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1642421747 Apr 01, 2015 (144)
29 EVA_EXAC ss1685263128 Apr 01, 2015 (144)
30 EVA_MGP ss1710885694 Apr 01, 2015 (144)
31 WEILL_CORNELL_DGM ss1917992179 Feb 12, 2016 (147)
32 GENOMED ss1966671433 Jul 19, 2016 (147)
33 JJLAB ss2019512269 Sep 14, 2016 (149)
34 USC_VALOUEV ss2147502627 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2159575842 Dec 20, 2016 (150)
36 TOPMED ss2321730742 Dec 20, 2016 (150)
37 SYSTEMSBIOZJU ss2624271904 Nov 08, 2017 (151)
38 GRF ss2697396680 Nov 08, 2017 (151)
39 GNOMAD ss2731058816 Nov 08, 2017 (151)
40 GNOMAD ss2746195796 Nov 08, 2017 (151)
41 GNOMAD ss2750973899 Nov 08, 2017 (151)
42 SWEGEN ss2986201590 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3023519758 Nov 08, 2017 (151)
44 TOPMED ss3067129948 Nov 08, 2017 (151)
45 TOPMED ss3067129949 Nov 08, 2017 (151)
46 CSHL ss3343289059 Nov 08, 2017 (151)
47 OMUKHERJEE_ADBS ss3646220223 Oct 11, 2018 (152)
48 EGCUT_WGS ss3654302801 Jul 12, 2019 (153)
49 EVA_DECODE ss3686047523 Jul 12, 2019 (153)
50 ACPOP ss3726740215 Jul 12, 2019 (153)
51 EVA ss3745755577 Jul 12, 2019 (153)
52 KHV_HUMAN_GENOMES ss3798777236 Jul 12, 2019 (153)
53 EVA ss3823550953 Apr 25, 2020 (154)
54 EVA ss3825994068 Apr 25, 2020 (154)
55 EVA ss3836384221 Apr 25, 2020 (154)
56 EVA ss3841788389 Apr 25, 2020 (154)
57 SGDP_PRJ ss3848069853 Apr 25, 2020 (154)
58 KRGDB ss3892931502 Apr 25, 2020 (154)
59 FSA-LAB ss3983913164 Apr 25, 2021 (155)
60 EVA ss3986095399 Apr 25, 2021 (155)
61 TOPMED ss4437310017 Apr 25, 2021 (155)
62 TOMMO_GENOMICS ss5142202346 Apr 25, 2021 (155)
63 1000Genomes NC_000001.10 - 3746583 Oct 11, 2018 (152)
64 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3746583 Oct 11, 2018 (152)
65 Genetic variation in the Estonian population NC_000001.10 - 3746583 Oct 11, 2018 (152)
66 ExAC NC_000001.10 - 3746583 Oct 11, 2018 (152)
67 The Danish reference pan genome NC_000001.10 - 3746583 Apr 25, 2020 (154)
68 gnomAD - Genomes NC_000001.11 - 3830019 Apr 25, 2021 (155)
69 gnomAD - Exomes NC_000001.10 - 3746583 Jul 12, 2019 (153)
70 GO Exome Sequencing Project NC_000001.10 - 3746583 Oct 11, 2018 (152)
71 Genome of the Netherlands Release 5 NC_000001.10 - 3746583 Apr 25, 2020 (154)
72 KOREAN population from KRGDB NC_000001.10 - 3746583 Apr 25, 2020 (154)
73 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 3746583 Apr 25, 2020 (154)
74 Northern Sweden NC_000001.10 - 3746583 Jul 12, 2019 (153)
75 Qatari NC_000001.10 - 3746583 Apr 25, 2020 (154)
76 SGDP_PRJ NC_000001.10 - 3746583 Apr 25, 2020 (154)
77 Siberian NC_000001.10 - 3746583 Apr 25, 2020 (154)
78 8.3KJPN NC_000001.10 - 3746583 Apr 25, 2021 (155)
79 TopMed NC_000001.11 - 3830019 Apr 25, 2021 (155)
80 UK 10K study - Twins NC_000001.10 - 3746583 Oct 11, 2018 (152)
81 ALFA NC_000001.11 - 3830019 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)
rs61622456 May 27, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
8834621937, ss3067129948 NC_000001.11:3830018:G:C NC_000001.11:3830018:G:C (self)
ss82870072 NC_000001.8:3769739:G:T NC_000001.11:3830018:G:T (self)
ss87174552, ss118453641, ss163005145, ss166008874, ss210455013, ss275691526, ss283991048, ss1584155412 NC_000001.9:3736442:G:T NC_000001.11:3830018:G:T (self)
120341, 53978, 41049, 4439529, 1367463, 73838, 9686, 23264, 108896, 2446, 25080, 34109, 86833, 18981, 171653, 53978, ss218203372, ss230404240, ss238123115, ss489716761, ss553734800, ss647536608, ss712268032, ss974796661, ss1289452300, ss1425693095, ss1573860229, ss1599427714, ss1642421747, ss1685263128, ss1710885694, ss1917992179, ss1966671433, ss2019512269, ss2147502627, ss2321730742, ss2624271904, ss2697396680, ss2731058816, ss2746195796, ss2750973899, ss2986201590, ss3343289059, ss3646220223, ss3654302801, ss3726740215, ss3745755577, ss3823550953, ss3825994068, ss3836384221, ss3848069853, ss3892931502, ss3983913164, ss3986095399, ss5142202346 NC_000001.10:3746582:G:T NC_000001.11:3830018:G:T (self)
867279, 570564, 916352, 8834621937, ss2159575842, ss3023519758, ss3067129949, ss3686047523, ss3798777236, ss3841788389, ss4437310017 NC_000001.11:3830018:G:T NC_000001.11:3830018:G:T (self)
ss12992585 NT_004321.15:1053356:G:T NC_000001.11:3830018:G:T (self)
ss3212056, ss41339252, ss137763664, ss154559532, ss161249439 NT_004350.19:3225214:G:T NC_000001.11:3830018: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 rs2275828

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