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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.

rs4648410

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3815888 (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>A / C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.352786 (93379/264690, TOPMED)
C=0.349784 (48955/139958, GnomAD)
C=0.39901 (7116/17834, ALFA) (+ 14 more)
G=0.44564 (7469/16760, 8.3KJPN)
C=0.3438 (1722/5008, 1000G)
C=0.4339 (1944/4480, Estonian)
C=0.4502 (1735/3854, ALSPAC)
C=0.4560 (1691/3708, TWINSUK)
C=0.4577 (1341/2930, KOREAN)
C=0.4307 (789/1832, Korea1K)
C=0.439 (438/998, GoNL)
C=0.458 (275/600, NorthernSweden)
C=0.240 (109/454, SGDP_PRJ)
C=0.315 (68/216, Qatari)
C=0.343 (70/204, Vietnamese)
C=0.20 (10/50, Siberian)
C=0.40 (16/40, 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.3815888C>A
GRCh38.p13 chr 1 NC_000001.11:g.3815888C>G
GRCh37.p13 chr 1 NC_000001.10:g.3732452C>A
GRCh37.p13 chr 1 NC_000001.10:g.3732452C>G
CEP104 RefSeqGene NG_046726.1:g.46346G>T
CEP104 RefSeqGene NG_046726.1:g.46346G>C
Gene: CEP104, centrosomal protein 104 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CEP104 transcript NM_014704.4:c.2663-371G>T N/A Intron Variant
CEP104 transcript variant X2 XM_005244815.4:c.2771-371…

XM_005244815.4:c.2771-371G>T

N/A Intron Variant
CEP104 transcript variant X3 XM_011542474.3:c.2681-371…

XM_011542474.3:c.2681-371G>T

N/A Intron Variant
CEP104 transcript variant X7 XM_017002918.2:c.2489-371…

XM_017002918.2:c.2489-371G>T

N/A Intron Variant
CEP104 transcript variant X8 XM_017002919.2:c.2465-371…

XM_017002919.2:c.2465-371G>T

N/A Intron Variant
CEP104 transcript variant X1 XM_024451101.1:c.2789-371…

XM_024451101.1:c.2789-371G>T

N/A Intron Variant
CEP104 transcript variant X4 XM_024451102.1:c.2615-371…

XM_024451102.1:c.2615-371G>T

N/A Intron Variant
CEP104 transcript variant X5 XM_024451103.1:c.2597-371…

XM_024451103.1:c.2597-371G>T

N/A Intron Variant
CEP104 transcript variant X6 XM_024451104.1:c.2591-371…

XM_024451104.1:c.2591-371G>T

N/A Intron Variant
CEP104 transcript variant X9 XM_024451106.1:c.2417-371…

XM_024451106.1:c.2417-371G>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 17834 C=0.39901 A=0.00000, G=0.60099
European Sub 13746 C=0.44340 A=0.00000, G=0.55660
African Sub 2434 C=0.1413 A=0.0000, G=0.8587
African Others Sub 90 C=0.04 A=0.00, G=0.96
African American Sub 2344 C=0.1451 A=0.0000, G=0.8549
Asian Sub 112 C=0.509 A=0.000, G=0.491
East Asian Sub 86 C=0.49 A=0.00, G=0.51
Other Asian Sub 26 C=0.58 A=0.00, G=0.42
Latin American 1 Sub 146 C=0.342 A=0.000, G=0.658
Latin American 2 Sub 610 C=0.467 A=0.000, G=0.533
South Asian Sub 98 C=0.27 A=0.00, G=0.73
Other Sub 688 C=0.376 A=0.000, G=0.624


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=0.352786 G=0.647214
gnomAD - Genomes Global Study-wide 139958 C=0.349784 G=0.650216
gnomAD - Genomes European Sub 75804 C=0.43535 G=0.56465
gnomAD - Genomes African Sub 41942 C=0.14286 G=0.85714
gnomAD - Genomes American Sub 13618 C=0.49075 G=0.50925
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.3422 G=0.6578
gnomAD - Genomes East Asian Sub 3128 C=0.4204 G=0.5796
gnomAD - Genomes Other Sub 2146 C=0.3858 G=0.6142
8.3KJPN JAPANESE Study-wide 16760 C=0.55436 G=0.44564
1000Genomes Global Study-wide 5008 C=0.3438 G=0.6562
1000Genomes African Sub 1322 C=0.0877 G=0.9123
1000Genomes East Asian Sub 1008 C=0.4266 G=0.5734
1000Genomes Europe Sub 1006 C=0.4573 G=0.5427
1000Genomes South Asian Sub 978 C=0.350 G=0.650
1000Genomes American Sub 694 C=0.539 G=0.461
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.4339 G=0.5661
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.4502 G=0.5498
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.4560 G=0.5440
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.4577 G=0.5423
Korean Genome Project KOREAN Study-wide 1832 C=0.4307 G=0.5693
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.439 G=0.561
Northern Sweden ACPOP Study-wide 600 C=0.458 G=0.542
SGDP_PRJ Global Study-wide 454 C=0.240 G=0.760
Qatari Global Study-wide 216 C=0.315 G=0.685
A Vietnamese Genetic Variation Database Global Study-wide 204 C=0.343 G=0.657
Siberian Global Study-wide 50 C=0.20 G=0.80
The Danish reference pan genome Danish Study-wide 40 C=0.40 G=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 C= A G
GRCh38.p13 chr 1 NC_000001.11:g.3815888= NC_000001.11:g.3815888C>A NC_000001.11:g.3815888C>G
GRCh37.p13 chr 1 NC_000001.10:g.3732452= NC_000001.10:g.3732452C>A NC_000001.10:g.3732452C>G
CEP104 RefSeqGene NG_046726.1:g.46346= NG_046726.1:g.46346G>T NG_046726.1:g.46346G>C
CEP104 transcript NM_014704.3:c.2663-371= NM_014704.3:c.2663-371G>T NM_014704.3:c.2663-371G>C
CEP104 transcript NM_014704.4:c.2663-371= NM_014704.4:c.2663-371G>T NM_014704.4:c.2663-371G>C
CEP104 transcript variant X1 XM_005244815.1:c.2771-371= XM_005244815.1:c.2771-371G>T XM_005244815.1:c.2771-371G>C
CEP104 transcript variant X2 XM_005244815.4:c.2771-371= XM_005244815.4:c.2771-371G>T XM_005244815.4:c.2771-371G>C
CEP104 transcript variant X3 XM_011542474.3:c.2681-371= XM_011542474.3:c.2681-371G>T XM_011542474.3:c.2681-371G>C
CEP104 transcript variant X7 XM_017002918.2:c.2489-371= XM_017002918.2:c.2489-371G>T XM_017002918.2:c.2489-371G>C
CEP104 transcript variant X8 XM_017002919.2:c.2465-371= XM_017002919.2:c.2465-371G>T XM_017002919.2:c.2465-371G>C
CEP104 transcript variant X1 XM_024451101.1:c.2789-371= XM_024451101.1:c.2789-371G>T XM_024451101.1:c.2789-371G>C
CEP104 transcript variant X4 XM_024451102.1:c.2615-371= XM_024451102.1:c.2615-371G>T XM_024451102.1:c.2615-371G>C
CEP104 transcript variant X5 XM_024451103.1:c.2597-371= XM_024451103.1:c.2597-371G>T XM_024451103.1:c.2597-371G>C
CEP104 transcript variant X6 XM_024451104.1:c.2591-371= XM_024451104.1:c.2591-371G>T XM_024451104.1:c.2591-371G>C
CEP104 transcript variant X9 XM_024451106.1:c.2417-371= XM_024451106.1:c.2417-371G>T XM_024451106.1:c.2417-371G>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#.

57 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6396450 Feb 20, 2003 (111)
2 BCM_SSAHASNP ss9872012 Jul 11, 2003 (116)
3 SC_SNP ss12992570 Dec 05, 2003 (119)
4 SSAHASNP ss20484906 Apr 05, 2004 (121)
5 HGSV ss78701865 Dec 06, 2007 (129)
6 HGSV ss84605834 Dec 15, 2007 (130)
7 BCMHGSC_JDW ss87174388 Mar 23, 2008 (129)
8 HUMANGENOME_JCVI ss97915484 Feb 05, 2009 (130)
9 COMPLETE_GENOMICS ss163004836 Jul 04, 2010 (132)
10 COMPLETE_GENOMICS ss163738071 Jul 04, 2010 (132)
11 BUSHMAN ss197925041 Jul 04, 2010 (132)
12 BL ss252880399 May 09, 2011 (134)
13 GMI ss275691457 May 04, 2012 (137)
14 GMI ss283991013 Apr 25, 2013 (138)
15 PJP ss290498318 May 09, 2011 (134)
16 1000GENOMES ss328376561 May 09, 2011 (134)
17 TISHKOFF ss553734701 Apr 25, 2013 (138)
18 SSMP ss647536487 Apr 25, 2013 (138)
19 EVA-GONL ss974796480 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1067627315 Aug 21, 2014 (142)
21 1000GENOMES ss1289451789 Aug 21, 2014 (142)
22 DDI ss1425693014 Apr 01, 2015 (144)
23 EVA_GENOME_DK ss1573860149 Apr 01, 2015 (144)
24 EVA_DECODE ss1584155260 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1599427413 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1642421446 Apr 01, 2015 (144)
27 HAMMER_LAB ss1793785122 Sep 08, 2015 (146)
28 WEILL_CORNELL_DGM ss1917992017 Feb 12, 2016 (147)
29 GENOMED ss1966671380 Jul 19, 2016 (147)
30 JJLAB ss2019512157 Sep 14, 2016 (149)
31 USC_VALOUEV ss2147502537 Dec 20, 2016 (150)
32 HUMAN_LONGEVITY ss2159574867 Dec 20, 2016 (150)
33 TOPMED ss2321729819 Dec 20, 2016 (150)
34 SYSTEMSBIOZJU ss2624271836 Nov 08, 2017 (151)
35 GRF ss2697396570 Nov 08, 2017 (151)
36 GNOMAD ss2750972626 Nov 08, 2017 (151)
37 SWEGEN ss2986201367 Nov 08, 2017 (151)
38 BIOINF_KMB_FNS_UNIBA ss3023519697 Nov 08, 2017 (151)
39 TOPMED ss3067127230 Nov 08, 2017 (151)
40 CSHL ss3343288960 Nov 08, 2017 (151)
41 URBANLAB ss3646586756 Oct 11, 2018 (152)
42 EGCUT_WGS ss3654302591 Jul 12, 2019 (153)
43 EVA_DECODE ss3686047262 Jul 12, 2019 (153)
44 ACPOP ss3726740066 Jul 12, 2019 (153)
45 EVA ss3745755368 Jul 12, 2019 (153)
46 PACBIO ss3783308790 Jul 12, 2019 (153)
47 PACBIO ss3788985671 Jul 12, 2019 (153)
48 PACBIO ss3793858301 Jul 12, 2019 (153)
49 KHV_HUMAN_GENOMES ss3798777048 Jul 12, 2019 (153)
50 EVA ss3825993986 Apr 25, 2020 (154)
51 EVA ss3836384167 Apr 25, 2020 (154)
52 EVA ss3841788331 Apr 25, 2020 (154)
53 SGDP_PRJ ss3848069587 Apr 25, 2020 (154)
54 KRGDB ss3892931164 Apr 25, 2020 (154)
55 KOGIC ss3943692951 Apr 25, 2020 (154)
56 TOPMED ss4437306334 Apr 25, 2021 (155)
57 TOMMO_GENOMICS ss5142201817 Apr 25, 2021 (155)
58 1000Genomes NC_000001.10 - 3732452 Oct 11, 2018 (152)
59 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3732452 Oct 11, 2018 (152)
60 Genetic variation in the Estonian population NC_000001.10 - 3732452 Oct 11, 2018 (152)
61 The Danish reference pan genome NC_000001.10 - 3732452 Apr 25, 2020 (154)
62 gnomAD - Genomes NC_000001.11 - 3815888 Apr 25, 2021 (155)
63 Genome of the Netherlands Release 5 NC_000001.10 - 3732452 Apr 25, 2020 (154)
64 KOREAN population from KRGDB NC_000001.10 - 3732452 Apr 25, 2020 (154)
65 Korean Genome Project NC_000001.11 - 3815888 Apr 25, 2020 (154)
66 Northern Sweden NC_000001.10 - 3732452 Jul 12, 2019 (153)
67 Qatari NC_000001.10 - 3732452 Apr 25, 2020 (154)
68 SGDP_PRJ NC_000001.10 - 3732452 Apr 25, 2020 (154)
69 Siberian NC_000001.10 - 3732452 Apr 25, 2020 (154)
70 8.3KJPN NC_000001.10 - 3732452 Apr 25, 2021 (155)
71 TopMed NC_000001.11 - 3815888 Apr 25, 2021 (155)
72 UK 10K study - Twins NC_000001.10 - 3732452 Oct 11, 2018 (152)
73 A Vietnamese Genetic Variation Database NC_000001.10 - 3732452 Jul 12, 2019 (153)
74 ALFA NC_000001.11 - 3815888 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)
rs59759587 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
10002908068 NC_000001.11:3815887:C:A NC_000001.11:3815887:C:A
ss78701865, ss84605834 NC_000001.8:3755608:C:G NC_000001.11:3815887:C:G (self)
ss87174388, ss163004836, ss163738071, ss197925041, ss252880399, ss275691457, ss283991013, ss290498318, ss1584155260 NC_000001.9:3722311:C:G NC_000001.11:3815887:C:G (self)
119820, 53658, 40839, 1367383, 23086, 108558, 24931, 33947, 86567, 18891, 171124, 53658, 11338, ss328376561, ss553734701, ss647536487, ss974796480, ss1067627315, ss1289451789, ss1425693014, ss1573860149, ss1599427413, ss1642421446, ss1793785122, ss1917992017, ss1966671380, ss2019512157, ss2147502537, ss2321729819, ss2624271836, ss2697396570, ss2750972626, ss2986201367, ss3343288960, ss3654302591, ss3726740066, ss3745755368, ss3783308790, ss3788985671, ss3793858301, ss3825993986, ss3836384167, ss3848069587, ss3892931164, ss5142201817 NC_000001.10:3732451:C:G NC_000001.11:3815887:C:G (self)
864296, 70952, 568181, 912669, 10002908068, ss2159574867, ss3023519697, ss3067127230, ss3646586756, ss3686047262, ss3798777048, ss3841788331, ss3943692951, ss4437306334 NC_000001.11:3815887:C:G NC_000001.11:3815887:C:G (self)
ss9872012, ss12992570, ss20484906 NT_004321.15:1039225:C:G NC_000001.11:3815887:C:G (self)
ss6396450, ss97915484 NT_004350.19:3211083:C:G NC_000001.11:3815887:C: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 rs4648410

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