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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs3747258

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr22:46686126 (GRCh38.p14) 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=0.154086 (40785/264690, TOPMED)
A=0.146744 (20553/140060, GnomAD)
A=0.00948 (268/28258, 14KJPN) (+ 17 more)
A=0.12296 (3323/27024, ALFA)
A=0.00996 (167/16760, 8.3KJPN)
A=0.1582 (1013/6404, 1000G_30x)
A=0.1518 (760/5008, 1000G)
A=0.0263 (118/4480, Estonian)
A=0.0423 (163/3854, ALSPAC)
A=0.0458 (170/3708, TWINSUK)
A=0.0024 (7/2922, KOREAN)
A=0.0016 (3/1832, Korea1K)
A=0.2019 (346/1714, HapMap)
A=0.059 (59/998, GoNL)
A=0.048 (29/600, NorthernSweden)
A=0.162 (35/216, Qatari)
G=0.43 (42/98, SGDP_PRJ)
A=0.05 (2/40, GENOME_DK)
G=0.5 (1/2, Siberian)
A=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CERK : 3 Prime UTR Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 27024 G=0.87704 A=0.12296
European Sub 18124 G=0.96187 A=0.03813
African Sub 6738 G=0.6453 A=0.3547
African Others Sub 232 G=0.578 A=0.422
African American Sub 6506 G=0.6477 A=0.3523
Asian Sub 124 G=0.992 A=0.008
East Asian Sub 96 G=0.99 A=0.01
Other Asian Sub 28 G=1.00 A=0.00
Latin American 1 Sub 168 G=0.911 A=0.089
Latin American 2 Sub 670 G=0.863 A=0.137
South Asian Sub 98 G=0.98 A=0.02
Other Sub 1102 G=0.8802 A=0.1198


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=0.845914 A=0.154086
gnomAD - Genomes Global Study-wide 140060 G=0.853256 A=0.146744
gnomAD - Genomes European Sub 75932 G=0.95646 A=0.04354
gnomAD - Genomes African Sub 41912 G=0.64001 A=0.35999
gnomAD - Genomes American Sub 13624 G=0.88080 A=0.11920
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.9226 A=0.0774
gnomAD - Genomes East Asian Sub 3126 G=0.9933 A=0.0067
gnomAD - Genomes Other Sub 2144 G=0.8801 A=0.1199
14KJPN JAPANESE Study-wide 28258 G=0.99052 A=0.00948
Allele Frequency Aggregator Total Global 27024 G=0.87704 A=0.12296
Allele Frequency Aggregator European Sub 18124 G=0.96187 A=0.03813
Allele Frequency Aggregator African Sub 6738 G=0.6453 A=0.3547
Allele Frequency Aggregator Other Sub 1102 G=0.8802 A=0.1198
Allele Frequency Aggregator Latin American 2 Sub 670 G=0.863 A=0.137
Allele Frequency Aggregator Latin American 1 Sub 168 G=0.911 A=0.089
Allele Frequency Aggregator Asian Sub 124 G=0.992 A=0.008
Allele Frequency Aggregator South Asian Sub 98 G=0.98 A=0.02
8.3KJPN JAPANESE Study-wide 16760 G=0.99004 A=0.00996
1000Genomes_30x Global Study-wide 6404 G=0.8418 A=0.1582
1000Genomes_30x African Sub 1786 G=0.5935 A=0.4065
1000Genomes_30x Europe Sub 1266 G=0.9613 A=0.0387
1000Genomes_30x South Asian Sub 1202 G=0.9276 A=0.0724
1000Genomes_30x East Asian Sub 1170 G=0.9906 A=0.0094
1000Genomes_30x American Sub 980 G=0.857 A=0.143
1000Genomes Global Study-wide 5008 G=0.8482 A=0.1518
1000Genomes African Sub 1322 G=0.5915 A=0.4085
1000Genomes East Asian Sub 1008 G=0.9901 A=0.0099
1000Genomes Europe Sub 1006 G=0.9642 A=0.0358
1000Genomes South Asian Sub 978 G=0.928 A=0.072
1000Genomes American Sub 694 G=0.850 A=0.150
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9737 A=0.0263
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9577 A=0.0423
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9542 A=0.0458
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9976 A=0.0024
Korean Genome Project KOREAN Study-wide 1832 G=0.9984 A=0.0016
HapMap Global Study-wide 1714 G=0.7981 A=0.2019
HapMap African Sub 690 G=0.622 A=0.378
HapMap American Sub 598 G=0.881 A=0.119
HapMap Asian Sub 252 G=0.980 A=0.020
HapMap Europe Sub 174 G=0.948 A=0.052
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.941 A=0.059
Northern Sweden ACPOP Study-wide 600 G=0.952 A=0.048
Qatari Global Study-wide 216 G=0.838 A=0.162
SGDP_PRJ Global Study-wide 98 G=0.43 A=0.57
The Danish reference pan genome Danish Study-wide 40 G=0.95 A=0.05
Siberian Global Study-wide 2 G=0.5 A=0.5
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.p14 chr 22 NC_000022.11:g.46686126G>A
GRCh37.p13 chr 22 NC_000022.10:g.47082023G>A
Gene: CERK, ceramide kinase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CERK transcript NM_022766.6:c.*1008= N/A 3 Prime UTR Variant
CERK transcript variant X2 XM_017028909.1:c.*1008= N/A 3 Prime UTR Variant
CERK transcript variant X1 XM_047441460.1:c.*1008= N/A 3 Prime UTR 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
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.p14 chr 22 NC_000022.11:g.46686126= NC_000022.11:g.46686126G>A
GRCh37.p13 chr 22 NC_000022.10:g.47082023= NC_000022.10:g.47082023G>A
CERK transcript NM_022766.6:c.*1008= NM_022766.6:c.*1008C>T
CERK transcript NM_022766.5:c.*1008= NM_022766.5:c.*1008C>T
CERK transcript variant X1 XM_047441460.1:c.*1008= XM_047441460.1:c.*1008C>T
CERK transcript variant X2 XM_017028909.1:c.*1008= XM_017028909.1:c.*1008C>T
CERK transcript variant 2 NM_182661.1:c.475= NM_182661.1:c.475C>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#.

70 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss4933280 Aug 28, 2002 (107)
2 PERLEGEN ss38338815 May 24, 2005 (125)
3 KRIBB_YJKIM ss65828307 Nov 29, 2006 (127)
4 PERLEGEN ss69270577 May 16, 2007 (127)
5 AFFY ss74812372 Aug 16, 2007 (128)
6 ILLUMINA ss74871426 Dec 06, 2007 (129)
7 SI_EXO ss76886587 Dec 06, 2007 (129)
8 HGSV ss78974979 Dec 06, 2007 (129)
9 HGSV ss83703336 Dec 14, 2007 (130)
10 BCMHGSC_JDW ss91944513 Mar 24, 2008 (129)
11 1000GENOMES ss114314546 Jan 25, 2009 (130)
12 ILLUMINA-UK ss117432211 Feb 14, 2009 (130)
13 KRIBB_YJKIM ss119459264 Dec 01, 2009 (131)
14 ENSEMBL ss138367007 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss168101955 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss169488894 Jul 04, 2010 (132)
17 ILLUMINA ss173621503 Jul 04, 2010 (132)
18 BUSHMAN ss204113157 Jul 04, 2010 (132)
19 1000GENOMES ss228720511 Jul 14, 2010 (132)
20 1000GENOMES ss238097523 Jul 15, 2010 (132)
21 ILLUMINA ss536027211 Sep 08, 2015 (146)
22 TISHKOFF ss566694901 Apr 25, 2013 (138)
23 SSMP ss662623439 Apr 25, 2013 (138)
24 EVA-GONL ss995434980 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1082716589 Aug 21, 2014 (142)
26 1000GENOMES ss1367490350 Aug 21, 2014 (142)
27 EVA_GENOME_DK ss1579783383 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1640163565 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1683157598 Apr 01, 2015 (144)
30 EVA_DECODE ss1699506111 Apr 01, 2015 (144)
31 EVA_SVP ss1713747049 Apr 01, 2015 (144)
32 HAMMER_LAB ss1809825757 Sep 08, 2015 (146)
33 WEILL_CORNELL_DGM ss1939006516 Feb 12, 2016 (147)
34 GENOMED ss1969287599 Jul 19, 2016 (147)
35 JJLAB ss2030275398 Sep 14, 2016 (149)
36 USC_VALOUEV ss2158898633 Dec 20, 2016 (150)
37 HUMAN_LONGEVITY ss2247993413 Dec 20, 2016 (150)
38 GRF ss2704651104 Nov 08, 2017 (151)
39 GNOMAD ss2975324674 Nov 08, 2017 (151)
40 SWEGEN ss3019439946 Nov 08, 2017 (151)
41 CSHL ss3352875661 Nov 08, 2017 (151)
42 ILLUMINA ss3628555100 Oct 12, 2018 (152)
43 ILLUMINA ss3638388395 Oct 12, 2018 (152)
44 ILLUMINA ss3643347524 Oct 12, 2018 (152)
45 OMUKHERJEE_ADBS ss3646569352 Oct 12, 2018 (152)
46 EGCUT_WGS ss3685929594 Jul 13, 2019 (153)
47 EVA_DECODE ss3708366122 Jul 13, 2019 (153)
48 ACPOP ss3744004359 Jul 13, 2019 (153)
49 EVA ss3759483596 Jul 13, 2019 (153)
50 KHV_HUMAN_GENOMES ss3822641601 Jul 13, 2019 (153)
51 EVA ss3825974439 Apr 27, 2020 (154)
52 EVA ss3836033232 Apr 27, 2020 (154)
53 SGDP_PRJ ss3890725344 Apr 27, 2020 (154)
54 KRGDB ss3941131517 Apr 27, 2020 (154)
55 KOGIC ss3983817887 Apr 27, 2020 (154)
56 EVA ss4017885444 Apr 27, 2021 (155)
57 TOPMED ss5112065130 Apr 27, 2021 (155)
58 TOMMO_GENOMICS ss5233019952 Apr 27, 2021 (155)
59 1000G_HIGH_COVERAGE ss5311394616 Oct 16, 2022 (156)
60 EVA ss5441839435 Oct 16, 2022 (156)
61 HUGCELL_USP ss5503207882 Oct 16, 2022 (156)
62 EVA ss5512401996 Oct 16, 2022 (156)
63 1000G_HIGH_COVERAGE ss5619083419 Oct 16, 2022 (156)
64 SANFORD_IMAGENETICS ss5664655168 Oct 16, 2022 (156)
65 TOMMO_GENOMICS ss5794270743 Oct 16, 2022 (156)
66 YY_MCH ss5818781601 Oct 16, 2022 (156)
67 EVA ss5822187032 Oct 16, 2022 (156)
68 EVA ss5853426777 Oct 16, 2022 (156)
69 EVA ss5882149073 Oct 16, 2022 (156)
70 EVA ss5959513671 Oct 16, 2022 (156)
71 1000Genomes NC_000022.10 - 47082023 Oct 12, 2018 (152)
72 1000Genomes_30x NC_000022.11 - 46686126 Oct 16, 2022 (156)
73 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 47082023 Oct 12, 2018 (152)
74 Genetic variation in the Estonian population NC_000022.10 - 47082023 Oct 12, 2018 (152)
75 The Danish reference pan genome NC_000022.10 - 47082023 Apr 27, 2020 (154)
76 gnomAD - Genomes NC_000022.11 - 46686126 Apr 27, 2021 (155)
77 Genome of the Netherlands Release 5 NC_000022.10 - 47082023 Apr 27, 2020 (154)
78 HapMap NC_000022.11 - 46686126 Apr 27, 2020 (154)
79 KOREAN population from KRGDB NC_000022.10 - 47082023 Apr 27, 2020 (154)
80 Korean Genome Project NC_000022.11 - 46686126 Apr 27, 2020 (154)
81 Northern Sweden NC_000022.10 - 47082023 Jul 13, 2019 (153)
82 Qatari NC_000022.10 - 47082023 Apr 27, 2020 (154)
83 SGDP_PRJ NC_000022.10 - 47082023 Apr 27, 2020 (154)
84 Siberian NC_000022.10 - 47082023 Apr 27, 2020 (154)
85 8.3KJPN NC_000022.10 - 47082023 Apr 27, 2021 (155)
86 14KJPN NC_000022.11 - 46686126 Oct 16, 2022 (156)
87 TopMed NC_000022.11 - 46686126 Apr 27, 2021 (155)
88 UK 10K study - Twins NC_000022.10 - 47082023 Oct 12, 2018 (152)
89 ALFA NC_000022.11 - 46686126 Apr 27, 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)
rs52789454 Sep 21, 2007 (128)
rs57724354 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78974979, ss83703336 NC_000022.8:45402541:G:A NC_000022.11:46686125:G:A (self)
ss91944513, ss114314546, ss117432211, ss168101955, ss169488894, ss204113157, ss1699506111, ss1713747049, ss3643347524 NC_000022.9:45460686:G:A NC_000022.11:46686125:G:A (self)
81054161, 44835326, 31667842, 5948322, 19974618, 48308911, 17289224, 21048438, 42742324, 11414987, 90989259, 44835326, ss228720511, ss238097523, ss536027211, ss566694901, ss662623439, ss995434980, ss1082716589, ss1367490350, ss1579783383, ss1640163565, ss1683157598, ss1809825757, ss1939006516, ss1969287599, ss2030275398, ss2158898633, ss2704651104, ss2975324674, ss3019439946, ss3352875661, ss3628555100, ss3638388395, ss3646569352, ss3685929594, ss3744004359, ss3759483596, ss3825974439, ss3836033232, ss3890725344, ss3941131517, ss4017885444, ss5233019952, ss5441839435, ss5512401996, ss5664655168, ss5822187032, ss5959513671 NC_000022.10:47082022:G:A NC_000022.11:46686125:G:A (self)
106609354, 572346421, 2271892, 40195888, 128107847, 387174077, 13011961999, ss2247993413, ss3708366122, ss3822641601, ss3983817887, ss5112065130, ss5311394616, ss5503207882, ss5619083419, ss5794270743, ss5818781601, ss5853426777, ss5882149073 NC_000022.11:46686125:G:A NC_000022.11:46686125:G:A (self)
ss4933280, ss38338815, ss65828307, ss69270577, ss74812372, ss74871426, ss119459264, ss138367007, ss173621503 NT_011520.12:26472591:G:A NC_000022.11:46686125:G:A (self)
ss76886587 NT_011523.11:2352728:G:A NC_000022.11:46686125: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 rs3747258

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.post761+d5e8e07