Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

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.

rs12025928

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:611317 (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
A>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.078478 (8252/105150, GnomAD)
A=0.00183 (45/24550, 14KJPN)
A=0.00897 (132/14720, 8.3KJPN) (+ 5 more)
A=0.07767 (860/11072, ALFA)
A=0.0123 (34/2754, KOREAN)
A=0.0024 (4/1642, Korea1K)
A=0.128 (75/584, NorthernSweden)
A=0.033 (17/510, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105378947 : 2KB Upstream 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 11072 A=0.07767 C=0.00000, G=0.92233, T=0.00000
European Sub 7118 A=0.0990 C=0.0000, G=0.9010, T=0.0000
African Sub 2342 A=0.0290 C=0.0000, G=0.9710, T=0.0000
African Others Sub 84 A=0.01 C=0.00, G=0.99, T=0.00
African American Sub 2258 A=0.0297 C=0.0000, G=0.9703, T=0.0000
Asian Sub 108 A=0.000 C=0.000, G=1.000, T=0.000
East Asian Sub 84 A=0.00 C=0.00, G=1.00, T=0.00
Other Asian Sub 24 A=0.00 C=0.00, G=1.00, T=0.00
Latin American 1 Sub 146 A=0.068 C=0.000, G=0.932, T=0.000
Latin American 2 Sub 610 A=0.054 C=0.000, G=0.946, T=0.000
South Asian Sub 94 A=0.03 C=0.00, G=0.97, T=0.00
Other Sub 654 A=0.063 C=0.000, G=0.937, T=0.000


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 105150 A=0.078478 G=0.921522
gnomAD - Genomes European Sub 63912 A=0.09790 G=0.90210
gnomAD - Genomes African Sub 23176 A=0.02912 G=0.97088
gnomAD - Genomes American Sub 11114 A=0.07252 G=0.92748
gnomAD - Genomes Ashkenazi Jewish Sub 2858 A=0.1319 G=0.8681
gnomAD - Genomes East Asian Sub 2500 A=0.0004 G=0.9996
gnomAD - Genomes Other Sub 1590 A=0.0855 G=0.9145
14KJPN JAPANESE Study-wide 24550 A=0.00183 G=0.99817
8.3KJPN JAPANESE Study-wide 14720 A=0.00897 G=0.99103
Allele Frequency Aggregator Total Global 11072 A=0.07767 C=0.00000, G=0.92233, T=0.00000
Allele Frequency Aggregator European Sub 7118 A=0.0990 C=0.0000, G=0.9010, T=0.0000
Allele Frequency Aggregator African Sub 2342 A=0.0290 C=0.0000, G=0.9710, T=0.0000
Allele Frequency Aggregator Other Sub 654 A=0.063 C=0.000, G=0.937, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.054 C=0.000, G=0.946, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.068 C=0.000, G=0.932, T=0.000
Allele Frequency Aggregator Asian Sub 108 A=0.000 C=0.000, G=1.000, T=0.000
Allele Frequency Aggregator South Asian Sub 94 A=0.03 C=0.00, G=0.97, T=0.00
KOREAN population from KRGDB KOREAN Study-wide 2754 A=0.0123 G=0.9877, T=0.0000
Korean Genome Project KOREAN Study-wide 1642 A=0.0024 G=0.9976
Northern Sweden ACPOP Study-wide 584 A=0.128 G=0.872
SGDP_PRJ Global Study-wide 510 A=0.033 G=0.967
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.611317A>C
GRCh38.p14 chr 1 NC_000001.11:g.611317A>G
GRCh38.p14 chr 1 NC_000001.11:g.611317A>T
GRCh37.p13 chr 1 NC_000001.10:g.546697A>C
GRCh37.p13 chr 1 NC_000001.10:g.546697A>G
GRCh37.p13 chr 1 NC_000001.10:g.546697A>T
Gene: LOC105378947, uncharacterized LOC105378947 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LOC105378947 transcript XM_011542538.1:c. N/A Upstream 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
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 A= C G T
GRCh38.p14 chr 1 NC_000001.11:g.611317= NC_000001.11:g.611317A>C NC_000001.11:g.611317A>G NC_000001.11:g.611317A>T
GRCh37.p13 chr 1 NC_000001.10:g.546697= NC_000001.10:g.546697A>C NC_000001.10:g.546697A>G NC_000001.10:g.546697A>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#.

36 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18078076 Feb 28, 2004 (120)
2 HGSV ss77293536 Dec 07, 2007 (129)
3 BCMHGSC_JDW ss87154959 Mar 23, 2008 (129)
4 ENSEMBL ss138944545 Dec 01, 2009 (147)
5 GMI ss154521981 Dec 01, 2009 (147)
6 ILLUMINA ss159200458 Dec 01, 2009 (147)
7 BUSHMAN ss197885280 Jul 04, 2010 (132)
8 BCM-HGSC-SUB ss205525275 Jul 04, 2010 (132)
9 BL ss252863975 May 09, 2011 (134)
10 GMI ss275680222 May 04, 2012 (137)
11 GMI ss283987271 Apr 25, 2013 (138)
12 SSMP ss647515442 Apr 25, 2013 (138)
13 ILLUMINA ss832712913 Jul 12, 2019 (153)
14 DDI ss1425684672 Apr 01, 2015 (144)
15 JJLAB ss2019498006 Sep 14, 2016 (149)
16 GRF ss2697373636 Nov 08, 2017 (151)
17 GNOMAD ss2750621308 Nov 08, 2017 (151)
18 SWEGEN ss2986145568 Nov 08, 2017 (151)
19 URBANLAB ss3646580994 Oct 11, 2018 (152)
20 ACPOP ss3726715667 Jul 12, 2019 (153)
21 PACBIO ss3783301728 Jul 12, 2019 (153)
22 PACBIO ss3788979708 Jul 12, 2019 (153)
23 PACBIO ss3793852275 Jul 12, 2019 (153)
24 EVA ss3825981358 Apr 25, 2020 (154)
25 SGDP_PRJ ss3847989862 Apr 25, 2020 (154)
26 KRGDB ss3892829794 Apr 25, 2020 (154)
27 KOGIC ss3943626334 Apr 25, 2020 (154)
28 TOMMO_GENOMICS ss5142043483 Apr 25, 2021 (155)
29 EVA ss5316176798 Oct 12, 2022 (156)
30 SANFORD_IMAGENETICS ss5624745867 Oct 12, 2022 (156)
31 TOMMO_GENOMICS ss5666180840 Oct 12, 2022 (156)
32 YY_MCH ss5800242271 Oct 12, 2022 (156)
33 EVA ss5831417265 Oct 12, 2022 (156)
34 EVA ss5848748788 Oct 12, 2022 (156)
35 EVA ss5979259101 Oct 12, 2022 (156)
36 EVA ss5979925952 Oct 12, 2022 (156)
37 gnomAD - Genomes NC_000001.11 - 611317 Apr 25, 2021 (155)
38 KOREAN population from KRGDB NC_000001.10 - 546697 Apr 25, 2020 (154)
39 Korean Genome Project NC_000001.11 - 611317 Apr 25, 2020 (154)
40 Northern Sweden NC_000001.10 - 546697 Jul 12, 2019 (153)
41 SGDP_PRJ NC_000001.10 - 546697 Apr 25, 2020 (154)
42 8.3KJPN NC_000001.10 - 546697 Apr 25, 2021 (155)
43 14KJPN NC_000001.11 - 611317 Oct 12, 2022 (156)
44 ALFA NC_000001.11 - 611317 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)
rs75351145 Jul 19, 2016 (147)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
5323117555 NC_000001.11:611316:A:C NC_000001.11:611316:A:C (self)
ss77293536 NC_000001.8:586559:A:G NC_000001.11:611316:A:G (self)
ss87154959, ss197885280, ss205525275, ss252863975, ss275680222, ss283987271 NC_000001.9:536559:A:G NC_000001.11:611316:A:G (self)
7188, 532, 6842, 12790, ss647515442, ss832712913, ss1425684672, ss2019498006, ss2697373636, ss2750621308, ss2986145568, ss3726715667, ss3783301728, ss3788979708, ss3793852275, ss3825981358, ss3847989862, ss3892829794, ss5142043483, ss5316176798, ss5624745867, ss5831417265, ss5979259101, ss5979925952 NC_000001.10:546696:A:G NC_000001.11:611316:A:G (self)
36480, 4335, 17944, 5323117555, ss3646580994, ss3943626334, ss5666180840, ss5800242271, ss5848748788 NC_000001.11:611316:A:G NC_000001.11:611316:A:G (self)
ss138944545, ss154521981, ss159200458 NT_004350.19:25328:A:G NC_000001.11:611316:A:G (self)
ss18078076 NT_034471.3:25328:A:G NC_000001.11:611316:A:G (self)
7188, ss3892829794 NC_000001.10:546696:A:T NC_000001.11:611316:A:T (self)
5323117555 NC_000001.11:611316:A:T NC_000001.11:611316:A: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 rs12025928

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