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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.

rs12116428

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:4994290 (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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.047093 (6598/140106, GnomAD)
T=0.05756 (3571/62042, ALFA)
T=0.07644 (2160/28258, 14KJPN) (+ 18 more)
T=0.07947 (1332/16760, 8.3KJPN)
T=0.0573 (367/6404, 1000G_30x)
T=0.0611 (306/5008, 1000G)
T=0.0576 (258/4480, Estonian)
T=0.0732 (282/3854, ALSPAC)
T=0.0674 (250/3708, TWINSUK)
T=0.0818 (239/2922, KOREAN)
T=0.0816 (170/2084, HGDP_Stanford)
T=0.0800 (96/1200, HapMap)
T=0.079 (79/998, GoNL)
T=0.055 (33/600, NorthernSweden)
T=0.083 (18/216, Qatari)
T=0.094 (20/212, Vietnamese)
C=0.46 (38/82, SGDP_PRJ)
T=0.07 (3/40, GENOME_DK)
C=0.50 (6/12, Siberian)
T=0.50 (6/12, Siberian)
T=0.0 (0/6, Ancient Sardinia)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC124904589 : Intron 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 62042 C=0.94244 G=0.00000, T=0.05756
European Sub 49854 C=0.93964 G=0.00000, T=0.06036
African Sub 4430 C=0.9935 G=0.0000, T=0.0065
African Others Sub 170 C=0.994 G=0.000, T=0.006
African American Sub 4260 C=0.9934 G=0.0000, T=0.0066
Asian Sub 162 C=0.969 G=0.000, T=0.031
East Asian Sub 124 C=0.968 G=0.000, T=0.032
Other Asian Sub 38 C=0.97 G=0.00, T=0.03
Latin American 1 Sub 234 C=0.983 G=0.000, T=0.017
Latin American 2 Sub 1186 C=0.9747 G=0.0000, T=0.0253
South Asian Sub 4858 C=0.9119 G=0.0000, T=0.0881
Other Sub 1318 C=0.9499 G=0.0000, T=0.0501


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
gnomAD - Genomes Global Study-wide 140106 C=0.952907 T=0.047093
gnomAD - Genomes European Sub 75846 C=0.93704 T=0.06296
gnomAD - Genomes African Sub 42010 C=0.98643 T=0.01357
gnomAD - Genomes American Sub 13646 C=0.95728 T=0.04272
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.9356 T=0.0644
gnomAD - Genomes East Asian Sub 3126 C=0.8887 T=0.1113
gnomAD - Genomes Other Sub 2154 C=0.9499 T=0.0501
Allele Frequency Aggregator Total Global 62042 C=0.94244 G=0.00000, T=0.05756
Allele Frequency Aggregator European Sub 49854 C=0.93964 G=0.00000, T=0.06036
Allele Frequency Aggregator South Asian Sub 4858 C=0.9119 G=0.0000, T=0.0881
Allele Frequency Aggregator African Sub 4430 C=0.9935 G=0.0000, T=0.0065
Allele Frequency Aggregator Other Sub 1318 C=0.9499 G=0.0000, T=0.0501
Allele Frequency Aggregator Latin American 2 Sub 1186 C=0.9747 G=0.0000, T=0.0253
Allele Frequency Aggregator Latin American 1 Sub 234 C=0.983 G=0.000, T=0.017
Allele Frequency Aggregator Asian Sub 162 C=0.969 G=0.000, T=0.031
14KJPN JAPANESE Study-wide 28258 C=0.92356 T=0.07644
8.3KJPN JAPANESE Study-wide 16760 C=0.92053 T=0.07947
1000Genomes_30x Global Study-wide 6404 C=0.9427 T=0.0573
1000Genomes_30x African Sub 1786 C=0.9994 T=0.0006
1000Genomes_30x Europe Sub 1266 C=0.9305 T=0.0695
1000Genomes_30x South Asian Sub 1202 C=0.9018 T=0.0982
1000Genomes_30x East Asian Sub 1170 C=0.8983 T=0.1017
1000Genomes_30x American Sub 980 C=0.958 T=0.042
1000Genomes Global Study-wide 5008 C=0.9389 T=0.0611
1000Genomes African Sub 1322 C=0.9992 T=0.0008
1000Genomes East Asian Sub 1008 C=0.8958 T=0.1042
1000Genomes Europe Sub 1006 C=0.9374 T=0.0626
1000Genomes South Asian Sub 978 C=0.893 T=0.107
1000Genomes American Sub 694 C=0.954 T=0.046
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9424 T=0.0576
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9268 T=0.0732
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9326 T=0.0674
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9182 T=0.0818
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 C=0.9184 T=0.0816
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 C=0.906 T=0.094
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 C=0.891 T=0.109
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 C=0.929 T=0.071
HGDP-CEPH-db Supplement 1 Europe Sub 320 C=0.906 T=0.094
HGDP-CEPH-db Supplement 1 Africa Sub 242 C=1.000 T=0.000
HGDP-CEPH-db Supplement 1 America Sub 216 C=0.944 T=0.056
HGDP-CEPH-db Supplement 1 Oceania Sub 72 C=0.81 T=0.19
HapMap Global Study-wide 1200 C=0.9200 T=0.0800
HapMap American Sub 670 C=0.912 T=0.088
HapMap Asian Sub 254 C=0.898 T=0.102
HapMap Europe Sub 176 C=0.943 T=0.057
HapMap African Sub 100 C=0.99 T=0.01
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.921 T=0.079
Northern Sweden ACPOP Study-wide 600 C=0.945 T=0.055
Qatari Global Study-wide 216 C=0.917 T=0.083
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.906 T=0.094
SGDP_PRJ Global Study-wide 82 C=0.46 T=0.54
The Danish reference pan genome Danish Study-wide 40 C=0.93 T=0.07
Siberian Global Study-wide 12 C=0.50 T=0.50
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 6 C=1.0 T=0.0
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 1 NC_000001.11:g.4994290C>G
GRCh38.p14 chr 1 NC_000001.11:g.4994290C>T
GRCh37.p13 chr 1 NC_000001.10:g.5054350C>G
GRCh37.p13 chr 1 NC_000001.10:g.5054350C>T
Gene: LOC124904589, uncharacterized LOC124904589 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC124904589 transcript XR_007067025.1:n. 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
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.p14 chr 1 NC_000001.11:g.4994290= NC_000001.11:g.4994290C>G NC_000001.11:g.4994290C>T
GRCh37.p13 chr 1 NC_000001.10:g.5054350= NC_000001.10:g.5054350C>G NC_000001.10:g.5054350C>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#.

74 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18243014 Feb 28, 2004 (120)
2 ILLUMINA ss66982905 Dec 01, 2006 (127)
3 ILLUMINA ss67156586 Dec 01, 2006 (127)
4 ILLUMINA ss68121594 Dec 12, 2006 (127)
5 ILLUMINA ss70555949 May 23, 2008 (130)
6 ILLUMINA ss71093261 May 18, 2007 (127)
7 ILLUMINA ss75607543 Dec 07, 2007 (129)
8 KRIBB_YJKIM ss85184606 Dec 14, 2007 (130)
9 BGI ss102715906 Dec 01, 2009 (131)
10 ILLUMINA ss153133779 Dec 01, 2009 (131)
11 ILLUMINA ss159204137 Dec 01, 2009 (131)
12 COMPLETE_GENOMICS ss163756856 Jul 04, 2010 (132)
13 COMPLETE_GENOMICS ss166031057 Jul 04, 2010 (132)
14 ILLUMINA ss171867654 Jul 04, 2010 (132)
15 1000GENOMES ss230409635 Jul 14, 2010 (132)
16 1000GENOMES ss238127788 Jul 15, 2010 (132)
17 ILLUMINA ss536755990 Sep 08, 2015 (146)
18 SSMP ss647544895 Apr 25, 2013 (138)
19 ILLUMINA ss832716578 Jul 12, 2019 (153)
20 EVA-GONL ss974808184 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1067636316 Aug 21, 2014 (142)
22 1000GENOMES ss1289492849 Aug 21, 2014 (142)
23 EVA_GENOME_DK ss1573865264 Apr 01, 2015 (144)
24 EVA_DECODE ss1584166922 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1599450309 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1642444342 Apr 01, 2015 (144)
27 EVA_SVP ss1712307833 Apr 01, 2015 (144)
28 WEILL_CORNELL_DGM ss1918004463 Feb 12, 2016 (147)
29 JJLAB ss2019518773 Sep 14, 2016 (149)
30 ILLUMINA ss2094782300 Dec 20, 2016 (150)
31 ILLUMINA ss2094950254 Dec 20, 2016 (150)
32 USC_VALOUEV ss2147510069 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2159657339 Dec 20, 2016 (150)
34 SYSTEMSBIOZJU ss2624275182 Nov 08, 2017 (151)
35 GRF ss2697404841 Nov 08, 2017 (151)
36 GNOMAD ss2751080590 Nov 08, 2017 (151)
37 SWEGEN ss2986218536 Nov 08, 2017 (151)
38 BIOINF_KMB_FNS_UNIBA ss3023523614 Nov 08, 2017 (151)
39 CSHL ss3343295358 Nov 08, 2017 (151)
40 ILLUMINA ss3626014780 Oct 11, 2018 (152)
41 ILLUMINA ss3637734446 Oct 11, 2018 (152)
42 ILLUMINA ss3638888685 Oct 11, 2018 (152)
43 ILLUMINA ss3639757212 Oct 11, 2018 (152)
44 ILLUMINA ss3642748583 Oct 11, 2018 (152)
45 ILLUMINA ss3643811123 Oct 11, 2018 (152)
46 ILLUMINA ss3651371497 Oct 11, 2018 (152)
47 EGCUT_WGS ss3654319892 Jul 12, 2019 (153)
48 EVA_DECODE ss3686068831 Jul 12, 2019 (153)
49 ACPOP ss3726750292 Jul 12, 2019 (153)
50 EVA ss3745770116 Jul 12, 2019 (153)
51 PACBIO ss3783312165 Jul 12, 2019 (153)
52 PACBIO ss3788988860 Jul 12, 2019 (153)
53 PACBIO ss3793861508 Jul 12, 2019 (153)
54 KHV_HUMAN_GENOMES ss3798791004 Jul 12, 2019 (153)
55 EVA ss3826000395 Apr 25, 2020 (154)
56 HGDP ss3847323041 Apr 25, 2020 (154)
57 SGDP_PRJ ss3848093224 Apr 25, 2020 (154)
58 KRGDB ss3892956533 Apr 25, 2020 (154)
59 EVA ss3984775847 Apr 25, 2021 (155)
60 EVA ss4016890784 Apr 25, 2021 (155)
61 TOPMED ss4437628104 Apr 25, 2021 (155)
62 TOPMED ss4437628105 Apr 25, 2021 (155)
63 TOMMO_GENOMICS ss5142247919 Apr 25, 2021 (155)
64 1000G_HIGH_COVERAGE ss5241004284 Oct 12, 2022 (156)
65 EVA ss5316440153 Oct 12, 2022 (156)
66 HUGCELL_USP ss5442226250 Oct 12, 2022 (156)
67 1000G_HIGH_COVERAGE ss5512686279 Oct 12, 2022 (156)
68 SANFORD_IMAGENETICS ss5624829949 Oct 12, 2022 (156)
69 TOMMO_GENOMICS ss5666475807 Oct 12, 2022 (156)
70 YY_MCH ss5800282076 Oct 12, 2022 (156)
71 EVA ss5831475272 Oct 12, 2022 (156)
72 EVA ss5848764943 Oct 12, 2022 (156)
73 EVA ss5906852681 Oct 12, 2022 (156)
74 EVA ss5936655992 Oct 12, 2022 (156)
75 1000Genomes NC_000001.10 - 5054350 Oct 11, 2018 (152)
76 1000Genomes_30x NC_000001.11 - 4994290 Oct 12, 2022 (156)
77 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 5054350 Oct 11, 2018 (152)
78 Genetic variation in the Estonian population NC_000001.10 - 5054350 Oct 11, 2018 (152)
79 The Danish reference pan genome NC_000001.10 - 5054350 Apr 25, 2020 (154)
80 gnomAD - Genomes NC_000001.11 - 4994290 Apr 25, 2021 (155)
81 Genome of the Netherlands Release 5 NC_000001.10 - 5054350 Apr 25, 2020 (154)
82 HGDP-CEPH-db Supplement 1 NC_000001.9 - 4954210 Apr 25, 2020 (154)
83 HapMap NC_000001.11 - 4994290 Apr 25, 2020 (154)
84 KOREAN population from KRGDB NC_000001.10 - 5054350 Apr 25, 2020 (154)
85 Northern Sweden NC_000001.10 - 5054350 Jul 12, 2019 (153)
86 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 5054350 Apr 25, 2021 (155)
87 Qatari NC_000001.10 - 5054350 Apr 25, 2020 (154)
88 SGDP_PRJ NC_000001.10 - 5054350 Apr 25, 2020 (154)
89 Siberian NC_000001.10 - 5054350 Apr 25, 2020 (154)
90 8.3KJPN NC_000001.10 - 5054350 Apr 25, 2021 (155)
91 14KJPN NC_000001.11 - 4994290 Oct 12, 2022 (156)
92 TopMed

Submission ignored due to conflicting rows:
Row 1234439 (NC_000001.11:4994289:C:G 1/264690)
Row 1234440 (NC_000001.11:4994289:C:T 12950/264690)

- Apr 25, 2021 (155)
93 TopMed

Submission ignored due to conflicting rows:
Row 1234439 (NC_000001.11:4994289:C:G 1/264690)
Row 1234440 (NC_000001.11:4994289:C:T 12950/264690)

- Apr 25, 2021 (155)
94 UK 10K study - Twins NC_000001.10 - 5054350 Oct 11, 2018 (152)
95 A Vietnamese Genetic Variation Database NC_000001.10 - 5054350 Jul 12, 2019 (153)
96 ALFA NC_000001.11 - 4994290 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)
rs57542220 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
4598715475, ss4437628104 NC_000001.11:4994289:C:G NC_000001.11:4994289:C:G (self)
ss3638888685, ss3639757212, ss3643811123 NC_000001.8:4964722:C:T NC_000001.11:4994289:C:T (self)
933, ss163756856, ss166031057, ss1584166922, ss1712307833, ss3642748583, ss3847323041 NC_000001.9:4954209:C:T NC_000001.11:4994289:C:T (self)
162158, 78460, 58140, 1372498, 34542, 133927, 35157, 1774, 46393, 110204, 26423, 217226, 78460, 17568, ss230409635, ss238127788, ss536755990, ss647544895, ss832716578, ss974808184, ss1067636316, ss1289492849, ss1573865264, ss1599450309, ss1642444342, ss1918004463, ss2019518773, ss2094782300, ss2094950254, ss2147510069, ss2624275182, ss2697404841, ss2751080590, ss2986218536, ss3343295358, ss3626014780, ss3637734446, ss3651371497, ss3654319892, ss3726750292, ss3745770116, ss3783312165, ss3788988860, ss3793861508, ss3826000395, ss3848093224, ss3892956533, ss3984775847, ss4016890784, ss5142247919, ss5316440153, ss5624829949, ss5831475272, ss5936655992 NC_000001.10:5054349:C:T NC_000001.11:4994289:C:T (self)
212214, 1134748, 5452, 312911, 4598715475, ss2159657339, ss3023523614, ss3686068831, ss3798791004, ss4437628105, ss5241004284, ss5442226250, ss5512686279, ss5666475807, ss5800282076, ss5848764943, ss5906852681 NC_000001.11:4994289:C:T NC_000001.11:4994289:C:T (self)
ss18243014 NT_004547.16:1057982:C:T NC_000001.11:4994289:C:T (self)
ss66982905, ss67156586, ss68121594, ss70555949, ss71093261, ss75607543, ss85184606, ss102715906, ss153133779, ss159204137, ss171867654 NT_021937.19:1059081:C:T NC_000001.11:4994289: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 rs12116428

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