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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.

rs4648417

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3830755 (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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.115981 (30699/264690, TOPMED)
T=0.112572 (14031/124640, GnomAD)
T=0.10003 (1873/18724, ALFA) (+ 13 more)
T=0.43313 (7254/16748, 8.3KJPN)
T=0.1651 (827/5008, 1000G)
T=0.1009 (450/4458, Estonian)
T=0.1144 (441/3854, ALSPAC)
T=0.1028 (381/3708, TWINSUK)
T=0.3414 (999/2926, KOREAN)
T=0.103 (103/998, GoNL)
T=0.120 (72/598, NorthernSweden)
T=0.120 (26/216, Qatari)
C=0.367 (66/180, SGDP_PRJ)
T=0.05 (2/40, GENOME_DK)
C=0.50 (7/14, Siberian)
T=0.50 (7/14, 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.3830755C>G
GRCh38.p13 chr 1 NC_000001.11:g.3830755C>T
GRCh37.p13 chr 1 NC_000001.10:g.3747319C>G
GRCh37.p13 chr 1 NC_000001.10:g.3747319C>T
CEP104 RefSeqGene NG_046726.1:g.31479G>C
CEP104 RefSeqGene NG_046726.1:g.31479G>A
Gene: CEP104, centrosomal protein 104 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CEP104 transcript NM_014704.4:c.1836+291G>C N/A Intron Variant
CEP104 transcript variant X2 XM_005244815.4:c.1944+291…

XM_005244815.4:c.1944+291G>C

N/A Intron Variant
CEP104 transcript variant X3 XM_011542474.3:c.1854+291…

XM_011542474.3:c.1854+291G>C

N/A Intron Variant
CEP104 transcript variant X7 XM_017002918.2:c.1662+291…

XM_017002918.2:c.1662+291G>C

N/A Intron Variant
CEP104 transcript variant X8 XM_017002919.2:c.1638+291…

XM_017002919.2:c.1638+291G>C

N/A Intron Variant
CEP104 transcript variant X1 XM_024451101.1:c.1962+291…

XM_024451101.1:c.1962+291G>C

N/A Intron Variant
CEP104 transcript variant X4 XM_024451102.1:c.1788+291…

XM_024451102.1:c.1788+291G>C

N/A Intron Variant
CEP104 transcript variant X5 XM_024451103.1:c.1770+291…

XM_024451103.1:c.1770+291G>C

N/A Intron Variant
CEP104 transcript variant X6 XM_024451104.1:c.1764+291…

XM_024451104.1:c.1764+291G>C

N/A Intron Variant
CEP104 transcript variant X9 XM_024451106.1:c.1590+291…

XM_024451106.1:c.1590+291G>C

N/A Intron Variant
CEP104 transcript variant X10 XM_024451108.1:c.1962+291…

XM_024451108.1:c.1962+291G>C

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 18724 C=0.89997 G=0.00000, T=0.10003
European Sub 14134 C=0.89416 G=0.00000, T=0.10584
African Sub 2934 C=0.9799 G=0.0000, T=0.0201
African Others Sub 112 C=1.000 G=0.000, T=0.000
African American Sub 2822 C=0.9791 G=0.0000, T=0.0209
Asian Sub 112 C=0.670 G=0.000, T=0.330
East Asian Sub 86 C=0.72 G=0.00, T=0.28
Other Asian Sub 26 C=0.50 G=0.00, T=0.50
Latin American 1 Sub 146 C=0.877 G=0.000, T=0.123
Latin American 2 Sub 610 C=0.736 G=0.000, T=0.264
South Asian Sub 98 C=0.88 G=0.00, T=0.12
Other Sub 690 C=0.870 G=0.000, T=0.130


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=0.884019 T=0.115981
gnomAD - Genomes Global Study-wide 124640 C=0.887428 T=0.112572
gnomAD - Genomes European Sub 69882 C=0.88161 T=0.11839
gnomAD - Genomes African Sub 35088 C=0.97102 T=0.02898
gnomAD - Genomes American Sub 11550 C=0.72667 T=0.27333
gnomAD - Genomes Ashkenazi Jewish Sub 3260 C=0.8813 T=0.1187
gnomAD - Genomes East Asian Sub 3028 C=0.6820 T=0.3180
gnomAD - Genomes Other Sub 1832 C=0.8723 T=0.1277
8.3KJPN JAPANESE Study-wide 16748 C=0.56687 T=0.43313
1000Genomes Global Study-wide 5008 C=0.8349 T=0.1651
1000Genomes African Sub 1322 C=0.9932 T=0.0068
1000Genomes East Asian Sub 1008 C=0.6627 T=0.3373
1000Genomes Europe Sub 1006 C=0.8887 T=0.1113
1000Genomes South Asian Sub 978 C=0.827 T=0.173
1000Genomes American Sub 694 C=0.716 T=0.284
Genetic variation in the Estonian population Estonian Study-wide 4458 C=0.8991 T=0.1009
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8856 T=0.1144
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8972 T=0.1028
KOREAN population from KRGDB KOREAN Study-wide 2926 C=0.6586 T=0.3414
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.897 T=0.103
Northern Sweden ACPOP Study-wide 598 C=0.880 T=0.120
Qatari Global Study-wide 216 C=0.880 T=0.120
SGDP_PRJ Global Study-wide 180 C=0.367 T=0.633
The Danish reference pan genome Danish Study-wide 40 C=0.95 T=0.05
Siberian Global Study-wide 14 C=0.50 T=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 C= G T
GRCh38.p13 chr 1 NC_000001.11:g.3830755= NC_000001.11:g.3830755C>G NC_000001.11:g.3830755C>T
GRCh37.p13 chr 1 NC_000001.10:g.3747319= NC_000001.10:g.3747319C>G NC_000001.10:g.3747319C>T
CEP104 RefSeqGene NG_046726.1:g.31479= NG_046726.1:g.31479G>C NG_046726.1:g.31479G>A
CEP104 transcript NM_014704.3:c.1836+291= NM_014704.3:c.1836+291G>C NM_014704.3:c.1836+291G>A
CEP104 transcript NM_014704.4:c.1836+291= NM_014704.4:c.1836+291G>C NM_014704.4:c.1836+291G>A
CEP104 transcript variant X1 XM_005244815.1:c.1944+291= XM_005244815.1:c.1944+291G>C XM_005244815.1:c.1944+291G>A
CEP104 transcript variant X2 XM_005244815.4:c.1944+291= XM_005244815.4:c.1944+291G>C XM_005244815.4:c.1944+291G>A
CEP104 transcript variant X3 XM_011542474.3:c.1854+291= XM_011542474.3:c.1854+291G>C XM_011542474.3:c.1854+291G>A
CEP104 transcript variant X7 XM_017002918.2:c.1662+291= XM_017002918.2:c.1662+291G>C XM_017002918.2:c.1662+291G>A
CEP104 transcript variant X8 XM_017002919.2:c.1638+291= XM_017002919.2:c.1638+291G>C XM_017002919.2:c.1638+291G>A
CEP104 transcript variant X1 XM_024451101.1:c.1962+291= XM_024451101.1:c.1962+291G>C XM_024451101.1:c.1962+291G>A
CEP104 transcript variant X4 XM_024451102.1:c.1788+291= XM_024451102.1:c.1788+291G>C XM_024451102.1:c.1788+291G>A
CEP104 transcript variant X5 XM_024451103.1:c.1770+291= XM_024451103.1:c.1770+291G>C XM_024451103.1:c.1770+291G>A
CEP104 transcript variant X6 XM_024451104.1:c.1764+291= XM_024451104.1:c.1764+291G>C XM_024451104.1:c.1764+291G>A
CEP104 transcript variant X9 XM_024451106.1:c.1590+291= XM_024451106.1:c.1590+291G>C XM_024451106.1:c.1590+291G>A
CEP104 transcript variant X10 XM_024451108.1:c.1962+291= XM_024451108.1:c.1962+291G>C XM_024451108.1:c.1962+291G>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#.

41 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss12992587 Dec 05, 2003 (119)
2 ABI ss41258258 Mar 13, 2006 (126)
3 HGSV ss78081845 Dec 06, 2007 (129)
4 GMI ss154559548 Dec 01, 2009 (131)
5 1000GENOMES ss230404247 Jul 14, 2010 (132)
6 GMI ss275691530 May 04, 2012 (137)
7 PJP ss290498370 May 09, 2011 (134)
8 TISHKOFF ss553734811 Apr 25, 2013 (138)
9 SSMP ss647536616 Apr 25, 2013 (138)
10 EVA-GONL ss974796673 Aug 21, 2014 (142)
11 JMKIDD_LAB ss1067627453 Aug 21, 2014 (142)
12 1000GENOMES ss1289452336 Aug 21, 2014 (142)
13 DDI ss1425693100 Apr 01, 2015 (144)
14 EVA_GENOME_DK ss1573860235 Apr 01, 2015 (144)
15 EVA_DECODE ss1584155424 Apr 01, 2015 (144)
16 EVA_UK10K_ALSPAC ss1599427728 Apr 01, 2015 (144)
17 EVA_UK10K_TWINSUK ss1642421761 Apr 01, 2015 (144)
18 WEILL_CORNELL_DGM ss1917992189 Feb 12, 2016 (147)
19 JJLAB ss2019512278 Sep 14, 2016 (149)
20 USC_VALOUEV ss2147502635 Dec 20, 2016 (150)
21 TOPMED ss2321730809 Dec 20, 2016 (150)
22 SYSTEMSBIOZJU ss2624271908 Nov 08, 2017 (151)
23 GRF ss2697396689 Nov 08, 2017 (151)
24 GNOMAD ss2750973981 Nov 08, 2017 (151)
25 SWEGEN ss2986201607 Nov 08, 2017 (151)
26 BIOINF_KMB_FNS_UNIBA ss3023519764 Nov 08, 2017 (151)
27 TOPMED ss3067130093 Nov 08, 2017 (151)
28 TOPMED ss3067130094 Nov 08, 2017 (151)
29 CSHL ss3343289066 Nov 08, 2017 (151)
30 EGCUT_WGS ss3654302819 Jul 12, 2019 (153)
31 EVA_DECODE ss3686047538 Jul 12, 2019 (153)
32 ACPOP ss3726740223 Jul 12, 2019 (153)
33 EVA ss3745755589 Jul 12, 2019 (153)
34 KHV_HUMAN_GENOMES ss3798777247 Jul 12, 2019 (153)
35 EVA ss3825994077 Apr 25, 2020 (154)
36 EVA ss3836384226 Apr 25, 2020 (154)
37 EVA ss3841788394 Apr 25, 2020 (154)
38 SGDP_PRJ ss3848069870 Apr 25, 2020 (154)
39 KRGDB ss3892931521 Apr 25, 2020 (154)
40 TOPMED ss4437310213 Apr 25, 2021 (155)
41 TOMMO_GENOMICS ss5142202372 Apr 25, 2021 (155)
42 1000Genomes NC_000001.10 - 3747319 Oct 11, 2018 (152)
43 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3747319 Oct 11, 2018 (152)
44 Genetic variation in the Estonian population NC_000001.10 - 3747319 Oct 11, 2018 (152)
45 The Danish reference pan genome NC_000001.10 - 3747319 Apr 25, 2020 (154)
46 gnomAD - Genomes NC_000001.11 - 3830755 Apr 25, 2021 (155)
47 Genome of the Netherlands Release 5 NC_000001.10 - 3747319 Apr 25, 2020 (154)
48 KOREAN population from KRGDB NC_000001.10 - 3747319 Apr 25, 2020 (154)
49 Northern Sweden NC_000001.10 - 3747319 Jul 12, 2019 (153)
50 Qatari NC_000001.10 - 3747319 Apr 25, 2020 (154)
51 SGDP_PRJ NC_000001.10 - 3747319 Apr 25, 2020 (154)
52 Siberian NC_000001.10 - 3747319 Apr 25, 2020 (154)
53 8.3KJPN NC_000001.10 - 3747319 Apr 25, 2021 (155)
54 TopMed NC_000001.11 - 3830755 Apr 25, 2021 (155)
55 UK 10K study - Twins NC_000001.10 - 3747319 Oct 11, 2018 (152)
56 ALFA NC_000001.11 - 3830755 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
14089304159, ss3067130093 NC_000001.11:3830754:C:G NC_000001.11:3830754:C:G (self)
ss78081845 NC_000001.8:3770475:C:T NC_000001.11:3830754:C:T (self)
ss275691530, ss290498370, ss1584155424 NC_000001.9:3737178:C:T NC_000001.11:3830754:C:T (self)
120377, 53993, 41067, 1367469, 23276, 108915, 25088, 34119, 86850, 18989, 171679, 53993, ss230404247, ss553734811, ss647536616, ss974796673, ss1067627453, ss1289452336, ss1425693100, ss1573860235, ss1599427728, ss1642421761, ss1917992189, ss2019512278, ss2147502635, ss2321730809, ss2624271908, ss2697396689, ss2750973981, ss2986201607, ss3343289066, ss3654302819, ss3726740223, ss3745755589, ss3825994077, ss3836384226, ss3848069870, ss3892931521, ss5142202372 NC_000001.10:3747318:C:T NC_000001.11:3830754:C:T (self)
867458, 570690, 916548, 14089304159, ss3023519764, ss3067130094, ss3686047538, ss3798777247, ss3841788394, ss4437310213 NC_000001.11:3830754:C:T NC_000001.11:3830754:C:T (self)
ss12992587 NT_004321.15:1054092:C:T NC_000001.11:3830754:C:T (self)
ss41258258, ss154559548 NT_004350.19:3225950:C:T NC_000001.11:3830754:C: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 rs4648417

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