Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs2027548

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3822948 (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=0.083671 (22147/264690, TOPMED)
A=0.068825 (9647/140168, GnomAD)
A=0.07037 (4738/67328, ALFA) (+ 18 more)
A=0.39839 (6677/16760, 8.3KJPN)
A=0.1967 (985/5008, 1000G)
A=0.0683 (306/4480, Estonian)
A=0.0527 (203/3854, ALSPAC)
A=0.0445 (165/3708, TWINSUK)
G=0.4986 (1461/2930, KOREAN)
A=0.2123 (442/2082, HGDP_Stanford)
A=0.1787 (336/1880, HapMap)
G=0.4782 (876/1832, Korea1K)
A=0.045 (45/998, GoNL)
A=0.063 (38/600, NorthernSweden)
A=0.011 (6/534, MGP)
A=0.093 (20/216, Qatari)
G=0.435 (94/216, Vietnamese)
G=0.351 (71/202, SGDP_PRJ)
A=0.03 (2/74, Ancient Sardinia)
A=0.12 (5/40, GENOME_DK)
G=0.44 (14/32, 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.3822948G>A
GRCh37.p13 chr 1 NC_000001.10:g.3739512G>A
CEP104 RefSeqGene NG_046726.1:g.39286C>T
Gene: CEP104, centrosomal protein 104 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CEP104 transcript NM_014704.4:c.2571+226C>T N/A Intron Variant
CEP104 transcript variant X2 XM_005244815.4:c.2679+226…

XM_005244815.4:c.2679+226C>T

N/A Intron Variant
CEP104 transcript variant X3 XM_011542474.3:c.2589+226…

XM_011542474.3:c.2589+226C>T

N/A Intron Variant
CEP104 transcript variant X7 XM_017002918.2:c.2397+226…

XM_017002918.2:c.2397+226C>T

N/A Intron Variant
CEP104 transcript variant X8 XM_017002919.2:c.2373+226…

XM_017002919.2:c.2373+226C>T

N/A Intron Variant
CEP104 transcript variant X1 XM_024451101.1:c.2697+226…

XM_024451101.1:c.2697+226C>T

N/A Intron Variant
CEP104 transcript variant X4 XM_024451102.1:c.2523+226…

XM_024451102.1:c.2523+226C>T

N/A Intron Variant
CEP104 transcript variant X5 XM_024451103.1:c.2505+226…

XM_024451103.1:c.2505+226C>T

N/A Intron Variant
CEP104 transcript variant X6 XM_024451104.1:c.2499+226…

XM_024451104.1:c.2499+226C>T

N/A Intron Variant
CEP104 transcript variant X9 XM_024451106.1:c.2325+226…

XM_024451106.1:c.2325+226C>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 67328 G=0.92963 A=0.07037
European Sub 54976 G=0.94978 A=0.05022
African Sub 4332 G=0.9582 A=0.0418
African Others Sub 170 G=0.982 A=0.018
African American Sub 4162 G=0.9572 A=0.0428
Asian Sub 188 G=0.585 A=0.415
East Asian Sub 148 G=0.574 A=0.426
Other Asian Sub 40 G=0.62 A=0.38
Latin American 1 Sub 254 G=0.909 A=0.091
Latin American 2 Sub 1224 G=0.8137 A=0.1863
South Asian Sub 4928 G=0.7297 A=0.2703
Other Sub 1426 G=0.9053 A=0.0947


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=0.916329 A=0.083671
gnomAD - Genomes Global Study-wide 140168 G=0.931175 A=0.068825
gnomAD - Genomes European Sub 75910 G=0.94421 A=0.05579
gnomAD - Genomes African Sub 42016 G=0.95792 A=0.04208
gnomAD - Genomes American Sub 13648 G=0.87661 A=0.12339
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.9639 A=0.0361
gnomAD - Genomes East Asian Sub 3120 G=0.4705 A=0.5295
gnomAD - Genomes Other Sub 2152 G=0.9126 A=0.0874
8.3KJPN JAPANESE Study-wide 16760 G=0.60161 A=0.39839
1000Genomes Global Study-wide 5008 G=0.8033 A=0.1967
1000Genomes African Sub 1322 G=0.9697 A=0.0303
1000Genomes East Asian Sub 1008 G=0.4792 A=0.5208
1000Genomes Europe Sub 1006 G=0.9443 A=0.0557
1000Genomes South Asian Sub 978 G=0.717 A=0.283
1000Genomes American Sub 694 G=0.875 A=0.125
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9317 A=0.0683
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9473 A=0.0527
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9555 A=0.0445
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.4986 A=0.5014
HGDP-CEPH-db Supplement 1 Global Study-wide 2082 G=0.7877 A=0.2123
HGDP-CEPH-db Supplement 1 Est_Asia Sub 468 G=0.515 A=0.485
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.795 A=0.205
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 G=0.960 A=0.040
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=0.972 A=0.028
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=0.950 A=0.050
HGDP-CEPH-db Supplement 1 America Sub 216 G=0.685 A=0.315
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=0.62 A=0.38
HapMap Global Study-wide 1880 G=0.8213 A=0.1787
HapMap American Sub 768 G=0.776 A=0.224
HapMap African Sub 682 G=0.957 A=0.043
HapMap Asian Sub 254 G=0.512 A=0.488
HapMap Europe Sub 176 G=0.938 A=0.062
Korean Genome Project KOREAN Study-wide 1832 G=0.4782 A=0.5218
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.955 A=0.045
Northern Sweden ACPOP Study-wide 600 G=0.937 A=0.063
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.989 A=0.011
Qatari Global Study-wide 216 G=0.907 A=0.093
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.435 A=0.565
SGDP_PRJ Global Study-wide 202 G=0.351 A=0.649
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 74 G=0.97 A=0.03
The Danish reference pan genome Danish Study-wide 40 G=0.88 A=0.12
Siberian Global Study-wide 32 G=0.44 A=0.56
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.3822948= NC_000001.11:g.3822948G>A
GRCh37.p13 chr 1 NC_000001.10:g.3739512= NC_000001.10:g.3739512G>A
CEP104 RefSeqGene NG_046726.1:g.39286= NG_046726.1:g.39286C>T
CEP104 transcript NM_014704.3:c.2571+226= NM_014704.3:c.2571+226C>T
CEP104 transcript NM_014704.4:c.2571+226= NM_014704.4:c.2571+226C>T
CEP104 transcript variant X1 XM_005244815.1:c.2679+226= XM_005244815.1:c.2679+226C>T
CEP104 transcript variant X2 XM_005244815.4:c.2679+226= XM_005244815.4:c.2679+226C>T
CEP104 transcript variant X3 XM_011542474.3:c.2589+226= XM_011542474.3:c.2589+226C>T
CEP104 transcript variant X7 XM_017002918.2:c.2397+226= XM_017002918.2:c.2397+226C>T
CEP104 transcript variant X8 XM_017002919.2:c.2373+226= XM_017002919.2:c.2373+226C>T
CEP104 transcript variant X1 XM_024451101.1:c.2697+226= XM_024451101.1:c.2697+226C>T
CEP104 transcript variant X4 XM_024451102.1:c.2523+226= XM_024451102.1:c.2523+226C>T
CEP104 transcript variant X5 XM_024451103.1:c.2505+226= XM_024451103.1:c.2505+226C>T
CEP104 transcript variant X6 XM_024451104.1:c.2499+226= XM_024451104.1:c.2499+226C>T
CEP104 transcript variant X9 XM_024451106.1:c.2325+226= XM_024451106.1:c.2325+226C>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#.

71 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2936065 Apr 12, 2001 (94)
2 YUSUKE ss4923595 Aug 28, 2002 (108)
3 SC_JCM ss5775184 Feb 20, 2003 (111)
4 WI_SSAHASNP ss11364154 Jul 11, 2003 (116)
5 SC_SNP ss12992582 Dec 05, 2003 (119)
6 ABI ss43979980 Mar 13, 2006 (126)
7 PERLEGEN ss46536855 Mar 13, 2006 (126)
8 ILLUMINA ss66610540 Nov 29, 2006 (127)
9 ILLUMINA ss67216565 Nov 29, 2006 (127)
10 ILLUMINA ss67610370 Nov 29, 2006 (127)
11 ILLUMINA ss70694830 May 24, 2008 (130)
12 ILLUMINA ss71260244 May 16, 2007 (127)
13 ILLUMINA ss75462106 Dec 07, 2007 (129)
14 ILLUMINA ss79108287 Dec 14, 2007 (130)
15 KRIBB_YJKIM ss83947974 Dec 14, 2007 (130)
16 BGI ss105114954 Dec 01, 2009 (131)
17 ILLUMINA ss121889155 Dec 01, 2009 (131)
18 ILLUMINA ss153820745 Dec 01, 2009 (131)
19 ILLUMINA ss159350255 Dec 01, 2009 (131)
20 ILLUMINA ss170955683 Jul 04, 2010 (132)
21 ILLUMINA ss173052765 Jul 04, 2010 (132)
22 BCM-HGSC-SUB ss205124046 Jul 04, 2010 (132)
23 1000GENOMES ss218203313 Jul 14, 2010 (132)
24 1000GENOMES ss230404197 Jul 14, 2010 (132)
25 1000GENOMES ss238123076 Jul 15, 2010 (132)
26 GMI ss275691491 May 04, 2012 (137)
27 GMI ss283991031 Apr 25, 2013 (138)
28 ILLUMINA ss537024853 Sep 08, 2015 (146)
29 TISHKOFF ss553734745 Apr 25, 2013 (138)
30 SSMP ss647536544 Apr 25, 2013 (138)
31 ILLUMINA ss825438805 Jul 19, 2016 (147)
32 ILLUMINA ss832862189 Jul 12, 2019 (153)
33 EVA-GONL ss974796563 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1067627373 Aug 21, 2014 (142)
35 1000GENOMES ss1289452035 Aug 21, 2014 (142)
36 EVA_GENOME_DK ss1573860178 Apr 01, 2015 (144)
37 EVA_DECODE ss1584155337 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1599427565 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1642421598 Apr 01, 2015 (144)
40 EVA_MGP ss1710885669 Apr 01, 2015 (144)
41 EVA_SVP ss1712306780 Apr 01, 2015 (144)
42 WEILL_CORNELL_DGM ss1917992096 Feb 12, 2016 (147)
43 GENOMED ss1966671404 Jul 19, 2016 (147)
44 JJLAB ss2019512209 Sep 14, 2016 (149)
45 USC_VALOUEV ss2147502582 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2159575379 Dec 20, 2016 (150)
47 TOPMED ss2321730295 Dec 20, 2016 (150)
48 SYSTEMSBIOZJU ss2624271868 Nov 08, 2017 (151)
49 GRF ss2697396621 Nov 08, 2017 (151)
50 GNOMAD ss2750973267 Nov 08, 2017 (151)
51 SWEGEN ss2986201476 Nov 08, 2017 (151)
52 TOPMED ss3067128603 Nov 08, 2017 (151)
53 CSHL ss3343289004 Nov 08, 2017 (151)
54 ILLUMINA ss3626011940 Oct 11, 2018 (152)
55 ILLUMINA ss3637733770 Oct 11, 2018 (152)
56 ILLUMINA ss3638888278 Oct 11, 2018 (152)
57 ILLUMINA ss3639440886 Oct 11, 2018 (152)
58 ILLUMINA ss3642747981 Oct 11, 2018 (152)
59 EGCUT_WGS ss3654302706 Jul 12, 2019 (153)
60 EVA_DECODE ss3686047400 Jul 12, 2019 (153)
61 ACPOP ss3726740135 Jul 12, 2019 (153)
62 EVA ss3745755470 Jul 12, 2019 (153)
63 KHV_HUMAN_GENOMES ss3798777132 Jul 12, 2019 (153)
64 HGDP ss3847322570 Apr 25, 2020 (154)
65 SGDP_PRJ ss3848069703 Apr 25, 2020 (154)
66 KRGDB ss3892931310 Apr 25, 2020 (154)
67 KOGIC ss3943693084 Apr 25, 2020 (154)
68 EVA ss3984774947 Apr 25, 2021 (155)
69 EVA ss4016890113 Apr 25, 2021 (155)
70 TOPMED ss4437308212 Apr 25, 2021 (155)
71 TOMMO_GENOMICS ss5142202079 Apr 25, 2021 (155)
72 1000Genomes NC_000001.10 - 3739512 Oct 11, 2018 (152)
73 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3739512 Oct 11, 2018 (152)
74 Genetic variation in the Estonian population NC_000001.10 - 3739512 Oct 11, 2018 (152)
75 The Danish reference pan genome NC_000001.10 - 3739512 Apr 25, 2020 (154)
76 gnomAD - Genomes NC_000001.11 - 3822948 Apr 25, 2021 (155)
77 Genome of the Netherlands Release 5 NC_000001.10 - 3739512 Apr 25, 2020 (154)
78 HGDP-CEPH-db Supplement 1 NC_000001.9 - 3729372 Apr 25, 2020 (154)
79 HapMap NC_000001.11 - 3822948 Apr 25, 2020 (154)
80 KOREAN population from KRGDB NC_000001.10 - 3739512 Apr 25, 2020 (154)
81 Korean Genome Project NC_000001.11 - 3822948 Apr 25, 2020 (154)
82 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 3739512 Apr 25, 2020 (154)
83 Northern Sweden NC_000001.10 - 3739512 Jul 12, 2019 (153)
84 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 3739512 Apr 25, 2021 (155)
85 Qatari NC_000001.10 - 3739512 Apr 25, 2020 (154)
86 SGDP_PRJ NC_000001.10 - 3739512 Apr 25, 2020 (154)
87 Siberian NC_000001.10 - 3739512 Apr 25, 2020 (154)
88 8.3KJPN NC_000001.10 - 3739512 Apr 25, 2021 (155)
89 TopMed NC_000001.11 - 3822948 Apr 25, 2021 (155)
90 UK 10K study - Twins NC_000001.10 - 3739512 Oct 11, 2018 (152)
91 A Vietnamese Genetic Variation Database NC_000001.10 - 3739512 Jul 12, 2019 (153)
92 ALFA NC_000001.11 - 3822948 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)
rs3737596 Oct 09, 2002 (108)
rs58179640 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638888278, ss3639440886 NC_000001.8:3762668:G:A NC_000001.11:3822947:G:A (self)
462, ss205124046, ss275691491, ss283991031, ss825438805, ss1584155337, ss1712306780, ss3642747981, ss3847322570 NC_000001.9:3729371:G:A NC_000001.11:3822947:G:A (self)
120069, 53820, 40954, 1367412, 23169, 108704, 2421, 25000, 874, 34026, 86683, 18936, 171386, 53820, 11385, ss218203313, ss230404197, ss238123076, ss537024853, ss553734745, ss647536544, ss832862189, ss974796563, ss1067627373, ss1289452035, ss1573860178, ss1599427565, ss1642421598, ss1710885669, ss1917992096, ss1966671404, ss2019512209, ss2147502582, ss2321730295, ss2624271868, ss2697396621, ss2750973267, ss2986201476, ss3343289004, ss3626011940, ss3637733770, ss3654302706, ss3726740135, ss3745755470, ss3848069703, ss3892931310, ss3984774947, ss4016890113, ss5142202079 NC_000001.10:3739511:G:A NC_000001.11:3822947:G:A (self)
865808, 2824, 71085, 569422, 914547, 5073236892, ss2159575379, ss3067128603, ss3686047400, ss3798777132, ss3943693084, ss4437308212 NC_000001.11:3822947:G:A NC_000001.11:3822947:G:A (self)
ss11364154, ss12992582 NT_004321.15:1046285:G:A NC_000001.11:3822947:G:A (self)
ss2936065, ss4923595, ss5775184, ss43979980, ss46536855, ss66610540, ss67216565, ss67610370, ss70694830, ss71260244, ss75462106, ss79108287, ss83947974, ss105114954, ss121889155, ss153820745, ss159350255, ss170955683, ss173052765 NT_004350.19:3218143:G:A NC_000001.11:3822947: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 rs2027548

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