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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.

rs4648345

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3826587 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.126412 (33460/264690, TOPMED)
A=0.130806 (18329/140124, GnomAD)
A=0.13431 (2547/18964, ALFA) (+ 17 more)
A=0.04708 (789/16760, 8.3KJPN)
A=0.1030 (516/5008, 1000G)
A=0.1431 (641/4480, Estonian)
A=0.1295 (499/3854, ALSPAC)
A=0.1343 (498/3708, TWINSUK)
A=0.0400 (117/2922, KOREAN)
A=0.0431 (79/1832, Korea1K)
A=0.124 (124/998, GoNL)
A=0.148 (89/600, NorthernSweden)
A=0.086 (46/534, MGP)
A=0.097 (32/330, HapMap)
A=0.185 (40/216, Qatari)
A=0.065 (14/214, Vietnamese)
G=0.47 (45/96, SGDP_PRJ)
A=0.12 (5/40, GENOME_DK)
G=0.5 (3/6, Siberian)
A=0.5 (3/6, 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.3826587G>A
GRCh37.p13 chr 1 NC_000001.10:g.3743151G>A
CEP104 RefSeqGene NG_046726.1:g.35647C>T
Gene: CEP104, centrosomal protein 104 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CEP104 transcript NM_014704.4:c.2188+121C>T N/A Intron Variant
CEP104 transcript variant X2 XM_005244815.4:c.2296+121…

XM_005244815.4:c.2296+121C>T

N/A Intron Variant
CEP104 transcript variant X3 XM_011542474.3:c.2206+121…

XM_011542474.3:c.2206+121C>T

N/A Intron Variant
CEP104 transcript variant X7 XM_017002918.2:c.2014+121…

XM_017002918.2:c.2014+121C>T

N/A Intron Variant
CEP104 transcript variant X8 XM_017002919.2:c.1990+121…

XM_017002919.2:c.1990+121C>T

N/A Intron Variant
CEP104 transcript variant X1 XM_024451101.1:c.2314+121…

XM_024451101.1:c.2314+121C>T

N/A Intron Variant
CEP104 transcript variant X4 XM_024451102.1:c.2140+121…

XM_024451102.1:c.2140+121C>T

N/A Intron Variant
CEP104 transcript variant X5 XM_024451103.1:c.2122+121…

XM_024451103.1:c.2122+121C>T

N/A Intron Variant
CEP104 transcript variant X6 XM_024451104.1:c.2116+121…

XM_024451104.1:c.2116+121C>T

N/A Intron Variant
CEP104 transcript variant X9 XM_024451106.1:c.1942+121…

XM_024451106.1:c.1942+121C>T

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 18964 G=0.86569 A=0.13431
European Sub 14336 G=0.86210 A=0.13790
African Sub 2960 G=0.8676 A=0.1324
African Others Sub 114 G=0.825 A=0.175
African American Sub 2846 G=0.8693 A=0.1307
Asian Sub 112 G=0.946 A=0.054
East Asian Sub 86 G=0.94 A=0.06
Other Asian Sub 26 G=0.96 A=0.04
Latin American 1 Sub 146 G=0.829 A=0.171
Latin American 2 Sub 610 G=0.921 A=0.079
South Asian Sub 98 G=0.84 A=0.16
Other Sub 702 G=0.882 A=0.118


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=0.873588 A=0.126412
gnomAD - Genomes Global Study-wide 140124 G=0.869194 A=0.130806
gnomAD - Genomes European Sub 75888 G=0.86491 A=0.13509
gnomAD - Genomes African Sub 41976 G=0.86411 A=0.13589
gnomAD - Genomes American Sub 13658 G=0.90357 A=0.09643
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.8049 A=0.1951
gnomAD - Genomes East Asian Sub 3132 G=0.9566 A=0.0434
gnomAD - Genomes Other Sub 2148 G=0.8734 A=0.1266
8.3KJPN JAPANESE Study-wide 16760 G=0.95292 A=0.04708
1000Genomes Global Study-wide 5008 G=0.8970 A=0.1030
1000Genomes African Sub 1322 G=0.8578 A=0.1422
1000Genomes East Asian Sub 1008 G=0.9514 A=0.0486
1000Genomes Europe Sub 1006 G=0.8588 A=0.1412
1000Genomes South Asian Sub 978 G=0.914 A=0.086
1000Genomes American Sub 694 G=0.924 A=0.076
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8569 A=0.1431
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8705 A=0.1295
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8657 A=0.1343
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9600 A=0.0400
Korean Genome Project KOREAN Study-wide 1832 G=0.9569 A=0.0431
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.876 A=0.124
Northern Sweden ACPOP Study-wide 600 G=0.852 A=0.148
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.914 A=0.086
HapMap Global Study-wide 330 G=0.903 A=0.097
HapMap African Sub 120 G=0.867 A=0.133
HapMap American Sub 120 G=0.883 A=0.117
HapMap Asian Sub 90 G=0.98 A=0.02
Qatari Global Study-wide 216 G=0.815 A=0.185
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.935 A=0.065
SGDP_PRJ Global Study-wide 96 G=0.47 A=0.53
The Danish reference pan genome Danish Study-wide 40 G=0.88 A=0.12
Siberian Global Study-wide 6 G=0.5 A=0.5
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
GRCh38.p13 chr 1 NC_000001.11:g.3826587= NC_000001.11:g.3826587G>A
GRCh37.p13 chr 1 NC_000001.10:g.3743151= NC_000001.10:g.3743151G>A
CEP104 RefSeqGene NG_046726.1:g.35647= NG_046726.1:g.35647C>T
CEP104 transcript NM_014704.3:c.2188+121= NM_014704.3:c.2188+121C>T
CEP104 transcript NM_014704.4:c.2188+121= NM_014704.4:c.2188+121C>T
CEP104 transcript variant X1 XM_005244815.1:c.2296+121= XM_005244815.1:c.2296+121C>T
CEP104 transcript variant X2 XM_005244815.4:c.2296+121= XM_005244815.4:c.2296+121C>T
CEP104 transcript variant X3 XM_011542474.3:c.2206+121= XM_011542474.3:c.2206+121C>T
CEP104 transcript variant X7 XM_017002918.2:c.2014+121= XM_017002918.2:c.2014+121C>T
CEP104 transcript variant X8 XM_017002919.2:c.1990+121= XM_017002919.2:c.1990+121C>T
CEP104 transcript variant X1 XM_024451101.1:c.2314+121= XM_024451101.1:c.2314+121C>T
CEP104 transcript variant X4 XM_024451102.1:c.2140+121= XM_024451102.1:c.2140+121C>T
CEP104 transcript variant X5 XM_024451103.1:c.2122+121= XM_024451103.1:c.2122+121C>T
CEP104 transcript variant X6 XM_024451104.1:c.2116+121= XM_024451104.1:c.2116+121C>T
CEP104 transcript variant X9 XM_024451106.1:c.1942+121= XM_024451106.1:c.1942+121C>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#.

54 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6396332 Feb 20, 2003 (111)
2 PERLEGEN ss24243622 Sep 20, 2004 (123)
3 ABI ss44032871 Mar 14, 2006 (126)
4 HUMANGENOME_JCVI ss99181291 Feb 06, 2009 (130)
5 ENSEMBL ss131785285 Dec 01, 2009 (131)
6 COMPLETE_GENOMICS ss163738449 Jul 04, 2010 (132)
7 BUSHMAN ss197925252 Jul 04, 2010 (132)
8 1000GENOMES ss218203337 Jul 14, 2010 (132)
9 1000GENOMES ss230404215 Jul 14, 2010 (132)
10 BL ss252880559 May 09, 2011 (134)
11 PJP ss290498351 May 09, 2011 (134)
12 GMI ss475580088 May 04, 2012 (137)
13 TISHKOFF ss553734768 Apr 25, 2013 (138)
14 SSMP ss647536579 Apr 25, 2013 (138)
15 EVA-GONL ss974796611 Aug 21, 2014 (142)
16 JMKIDD_LAB ss1067627401 Aug 21, 2014 (142)
17 1000GENOMES ss1289452176 Aug 21, 2014 (142)
18 EVA_GENOME_DK ss1573860200 Apr 01, 2015 (144)
19 EVA_DECODE ss1584155372 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1599427641 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1642421674 Apr 01, 2015 (144)
22 EVA_MGP ss1710885680 Apr 01, 2015 (144)
23 HAMMER_LAB ss1793785212 Sep 08, 2015 (146)
24 WEILL_CORNELL_DGM ss1917992138 Feb 12, 2016 (147)
25 JJLAB ss2019512234 Sep 14, 2016 (149)
26 USC_VALOUEV ss2147502601 Dec 20, 2016 (150)
27 HUMAN_LONGEVITY ss2159575616 Dec 20, 2016 (150)
28 TOPMED ss2321730511 Dec 20, 2016 (150)
29 GRF ss2697396652 Nov 08, 2017 (151)
30 GNOMAD ss2750973593 Nov 08, 2017 (151)
31 SWEGEN ss2986201537 Nov 08, 2017 (151)
32 BIOINF_KMB_FNS_UNIBA ss3023519737 Nov 08, 2017 (151)
33 TOPMED ss3067129322 Nov 08, 2017 (151)
34 CSHL ss3343289031 Nov 08, 2017 (151)
35 URBANLAB ss3646586798 Oct 11, 2018 (152)
36 EGCUT_WGS ss3654302744 Jul 12, 2019 (153)
37 EVA_DECODE ss3686047454 Jul 12, 2019 (153)
38 ACPOP ss3726740175 Jul 12, 2019 (153)
39 EVA ss3745755525 Jul 12, 2019 (153)
40 PACBIO ss3783308829 Jul 12, 2019 (153)
41 PACBIO ss3788985717 Jul 12, 2019 (153)
42 PACBIO ss3793858344 Jul 12, 2019 (153)
43 KHV_HUMAN_GENOMES ss3798777177 Jul 12, 2019 (153)
44 EVA ss3825994042 Apr 25, 2020 (154)
45 EVA ss3836384205 Apr 25, 2020 (154)
46 EVA ss3841788373 Apr 25, 2020 (154)
47 SGDP_PRJ ss3848069781 Apr 25, 2020 (154)
48 KRGDB ss3892931437 Apr 25, 2020 (154)
49 KOGIC ss3943693140 Apr 25, 2020 (154)
50 FSA-LAB ss3983913144 Apr 25, 2021 (155)
51 FSA-LAB ss3983913145 Apr 25, 2021 (155)
52 EVA ss3986095384 Apr 25, 2021 (155)
53 TOPMED ss4437309131 Apr 25, 2021 (155)
54 TOMMO_GENOMICS ss5142202229 Apr 25, 2021 (155)
55 1000Genomes NC_000001.10 - 3743151 Oct 11, 2018 (152)
56 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3743151 Oct 11, 2018 (152)
57 Genetic variation in the Estonian population NC_000001.10 - 3743151 Oct 11, 2018 (152)
58 The Danish reference pan genome NC_000001.10 - 3743151 Apr 25, 2020 (154)
59 gnomAD - Genomes NC_000001.11 - 3826587 Apr 25, 2021 (155)
60 Genome of the Netherlands Release 5 NC_000001.10 - 3743151 Apr 25, 2020 (154)
61 HapMap NC_000001.11 - 3826587 Apr 25, 2020 (154)
62 KOREAN population from KRGDB NC_000001.10 - 3743151 Apr 25, 2020 (154)
63 Korean Genome Project NC_000001.11 - 3826587 Apr 25, 2020 (154)
64 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 3743151 Apr 25, 2020 (154)
65 Northern Sweden NC_000001.10 - 3743151 Jul 12, 2019 (153)
66 Qatari NC_000001.10 - 3743151 Apr 25, 2020 (154)
67 SGDP_PRJ NC_000001.10 - 3743151 Apr 25, 2020 (154)
68 Siberian NC_000001.10 - 3743151 Apr 25, 2020 (154)
69 8.3KJPN NC_000001.10 - 3743151 Apr 25, 2021 (155)
70 TopMed NC_000001.11 - 3826587 Apr 25, 2021 (155)
71 UK 10K study - Twins NC_000001.10 - 3743151 Oct 11, 2018 (152)
72 A Vietnamese Genetic Variation Database NC_000001.10 - 3743151 Jul 12, 2019 (153)
73 ALFA NC_000001.11 - 3826587 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)
rs17411989 Oct 07, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss163738449, ss197925252, ss252880559, ss290498351, ss475580088, ss1584155372 NC_000001.9:3733010:G:A NC_000001.11:3826586:G:A (self)
120212, 53898, 40992, 1367434, 23214, 108831, 2432, 25040, 34068, 86761, 18955, 171536, 53898, 11408, ss218203337, ss230404215, ss553734768, ss647536579, ss974796611, ss1067627401, ss1289452176, ss1573860200, ss1599427641, ss1642421674, ss1710885680, ss1793785212, ss1917992138, ss2019512234, ss2147502601, ss2321730511, ss2697396652, ss2750973593, ss2986201537, ss3343289031, ss3654302744, ss3726740175, ss3745755525, ss3783308829, ss3788985717, ss3793858344, ss3825994042, ss3836384205, ss3848069781, ss3892931437, ss3983913144, ss3983913145, ss3986095384, ss5142202229 NC_000001.10:3743150:G:A NC_000001.11:3826586:G:A (self)
866589, 2836, 71141, 569987, 915466, 13536605322, ss2159575616, ss3023519737, ss3067129322, ss3646586798, ss3686047454, ss3798777177, ss3841788373, ss3943693140, ss4437309131 NC_000001.11:3826586:G:A NC_000001.11:3826586:G:A (self)
ss6396332, ss24243622, ss44032871, ss99181291, ss131785285 NT_004350.19:3221782:G:A NC_000001.11:3826586:G:A (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 rs4648345

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