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.

rs5744904

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:132648934 (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 / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000026 (7/264690, TOPMED)
A=0.000014 (2/140282, GnomAD)
A=0.000009 (1/108158, ALFA) (+ 4 more)
A=0.00053 (15/28258, 14KJPN)
A=0.00048 (8/16760, 8.3KJPN)
A=0.0007 (2/2920, KOREAN)
A=0.004 (3/724, HapMap)
Clinical Significance
Reported in ClinVar
Gene : Consequence
POLE : Missense 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 108158 G=0.999991 A=0.000009
European Sub 92868 G=0.99999 A=0.00001
African Sub 8870 G=1.0000 A=0.0000
African Others Sub 322 G=1.000 A=0.000
African American Sub 8548 G=1.0000 A=0.0000
Asian Sub 592 G=1.000 A=0.000
East Asian Sub 468 G=1.000 A=0.000
Other Asian Sub 124 G=1.000 A=0.000
Latin American 1 Sub 650 G=1.000 A=0.000
Latin American 2 Sub 2152 G=1.0000 A=0.0000
South Asian Sub 168 G=1.000 A=0.000
Other Sub 2858 G=1.0000 A=0.0000


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=0.999974 A=0.000026
gnomAD - Genomes Global Study-wide 140282 G=0.999986 A=0.000014
gnomAD - Genomes European Sub 75954 G=0.99999 A=0.00001
gnomAD - Genomes African Sub 42050 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13668 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=0.9997 A=0.0003
gnomAD - Genomes Other Sub 2152 G=1.0000 A=0.0000
Allele Frequency Aggregator Total Global 108158 G=0.999991 A=0.000009
Allele Frequency Aggregator European Sub 92868 G=0.99999 A=0.00001
Allele Frequency Aggregator African Sub 8870 G=1.0000 A=0.0000
Allele Frequency Aggregator Other Sub 2858 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 2152 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 1 Sub 650 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 592 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 168 G=1.000 A=0.000
14KJPN JAPANESE Study-wide 28258 G=0.99947 A=0.00053
8.3KJPN JAPANESE Study-wide 16760 G=0.99952 A=0.00048
KOREAN population from KRGDB KOREAN Study-wide 2920 G=0.9993 A=0.0007
HapMap Global Study-wide 724 G=0.996 A=0.004
HapMap American Sub 326 G=0.994 A=0.006
HapMap African Sub 226 G=0.996 A=0.004
HapMap Asian Sub 172 G=1.000 A=0.000
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 12 NC_000012.12:g.132648934G>A
GRCh38.p14 chr 12 NC_000012.12:g.132648934G>C
GRCh37.p13 chr 12 NC_000012.11:g.133225520G>A
GRCh37.p13 chr 12 NC_000012.11:g.133225520G>C
POLE RefSeqGene (LRG_789) NG_033840.1:g.43591C>T
POLE RefSeqGene (LRG_789) NG_033840.1:g.43591C>G
Gene: POLE, DNA polymerase epsilon, catalytic subunit (minus strand)
Molecule type Change Amino acid[Codon] SO Term
POLE transcript NM_006231.4:c.4144C>T R [CGC] > C [TGC] Coding Sequence Variant
DNA polymerase epsilon catalytic subunit A NP_006222.2:p.Arg1382Cys R (Arg) > C (Cys) Missense Variant
POLE transcript NM_006231.4:c.4144C>G R [CGC] > G [GGC] Coding Sequence Variant
DNA polymerase epsilon catalytic subunit A NP_006222.2:p.Arg1382Gly R (Arg) > G (Gly) Missense Variant
POLE transcript variant X1 XM_011534795.4:c.4144C>T R [CGC] > C [TGC] Coding Sequence Variant
DNA polymerase epsilon catalytic subunit A isoform X1 XP_011533097.1:p.Arg1382C…

XP_011533097.1:p.Arg1382Cys

R (Arg) > C (Cys) Missense Variant
POLE transcript variant X1 XM_011534795.4:c.4144C>G R [CGC] > G [GGC] Coding Sequence Variant
DNA polymerase epsilon catalytic subunit A isoform X1 XP_011533097.1:p.Arg1382G…

XP_011533097.1:p.Arg1382Gly

R (Arg) > G (Gly) Missense Variant
POLE transcript variant X2 XM_011534797.4:c.3223C>T R [CGC] > C [TGC] Coding Sequence Variant
DNA polymerase epsilon catalytic subunit A isoform X2 XP_011533099.1:p.Arg1075C…

XP_011533099.1:p.Arg1075Cys

R (Arg) > C (Cys) Missense Variant
POLE transcript variant X2 XM_011534797.4:c.3223C>G R [CGC] > G [GGC] Coding Sequence Variant
DNA polymerase epsilon catalytic subunit A isoform X2 XP_011533099.1:p.Arg1075G…

XP_011533099.1:p.Arg1075Gly

R (Arg) > G (Gly) Missense Variant
POLE transcript variant X3 XM_011534799.3:c.4144C>T R [CGC] > C [TGC] Coding Sequence Variant
DNA polymerase epsilon catalytic subunit A isoform X3 XP_011533101.1:p.Arg1382C…

XP_011533101.1:p.Arg1382Cys

R (Arg) > C (Cys) Missense Variant
POLE transcript variant X3 XM_011534799.3:c.4144C>G R [CGC] > G [GGC] Coding Sequence Variant
DNA polymerase epsilon catalytic subunit A isoform X3 XP_011533101.1:p.Arg1382G…

XP_011533101.1:p.Arg1382Gly

R (Arg) > G (Gly) Missense Variant
POLE transcript variant X4 XM_047429018.1:c.4144C>T R [CGC] > C [TGC] Coding Sequence Variant
DNA polymerase epsilon catalytic subunit A isoform X4 XP_047284974.1:p.Arg1382C…

XP_047284974.1:p.Arg1382Cys

R (Arg) > C (Cys) Missense Variant
POLE transcript variant X4 XM_047429018.1:c.4144C>G R [CGC] > G [GGC] Coding Sequence Variant
DNA polymerase epsilon catalytic subunit A isoform X4 XP_047284974.1:p.Arg1382G…

XP_047284974.1:p.Arg1382Gly

R (Arg) > G (Gly) Missense Variant
POLE transcript variant X6 XM_011534802.4:c.1132C>T R [CGC] > C [TGC] Coding Sequence Variant
DNA polymerase epsilon catalytic subunit A isoform X5 XP_011533104.1:p.Arg378Cys R (Arg) > C (Cys) Missense Variant
POLE transcript variant X6 XM_011534802.4:c.1132C>G R [CGC] > G [GGC] Coding Sequence Variant
DNA polymerase epsilon catalytic subunit A isoform X5 XP_011533104.1:p.Arg378Gly R (Arg) > G (Gly) Missense Variant
POLE transcript variant X5 XR_941395.3:n.4171C>T N/A Non Coding Transcript Variant
POLE transcript variant X5 XR_941395.3:n.4171C>G N/A Non Coding 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.

Allele: A (allele ID: 462535 )
ClinVar Accession Disease Names Clinical Significance
RCV000543275.6 Colorectal cancer, susceptibility to, 12 Uncertain-Significance
Allele: C (allele ID: 398771 )
ClinVar Accession Disease Names Clinical Significance
RCV000474418.5 Colorectal cancer, susceptibility to, 12 Uncertain-Significance
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 C
GRCh38.p14 chr 12 NC_000012.12:g.132648934= NC_000012.12:g.132648934G>A NC_000012.12:g.132648934G>C
GRCh37.p13 chr 12 NC_000012.11:g.133225520= NC_000012.11:g.133225520G>A NC_000012.11:g.133225520G>C
POLE RefSeqGene (LRG_789) NG_033840.1:g.43591= NG_033840.1:g.43591C>T NG_033840.1:g.43591C>G
POLE transcript NM_006231.4:c.4144= NM_006231.4:c.4144C>T NM_006231.4:c.4144C>G
POLE transcript NM_006231.3:c.4144= NM_006231.3:c.4144C>T NM_006231.3:c.4144C>G
POLE transcript NM_006231.2:c.4144= NM_006231.2:c.4144C>T NM_006231.2:c.4144C>G
POLE transcript variant X1 XM_011534795.4:c.4144= XM_011534795.4:c.4144C>T XM_011534795.4:c.4144C>G
POLE transcript variant X1 XM_011534795.3:c.4144= XM_011534795.3:c.4144C>T XM_011534795.3:c.4144C>G
POLE transcript variant X1 XM_011534795.2:c.4144= XM_011534795.2:c.4144C>T XM_011534795.2:c.4144C>G
POLE transcript variant X1 XM_011534795.1:c.4144= XM_011534795.1:c.4144C>T XM_011534795.1:c.4144C>G
POLE transcript variant X2 XM_011534797.4:c.3223= XM_011534797.4:c.3223C>T XM_011534797.4:c.3223C>G
POLE transcript variant X2 XM_011534797.3:c.3223= XM_011534797.3:c.3223C>T XM_011534797.3:c.3223C>G
POLE transcript variant X2 XM_011534797.2:c.3223= XM_011534797.2:c.3223C>T XM_011534797.2:c.3223C>G
POLE transcript variant X3 XM_011534797.1:c.3223= XM_011534797.1:c.3223C>T XM_011534797.1:c.3223C>G
POLE transcript variant X6 XM_011534802.4:c.1132= XM_011534802.4:c.1132C>T XM_011534802.4:c.1132C>G
POLE transcript variant X7 XM_011534802.3:c.1132= XM_011534802.3:c.1132C>T XM_011534802.3:c.1132C>G
POLE transcript variant X7 XM_011534802.2:c.1132= XM_011534802.2:c.1132C>T XM_011534802.2:c.1132C>G
POLE transcript variant X9 XM_011534802.1:c.1132= XM_011534802.1:c.1132C>T XM_011534802.1:c.1132C>G
POLE transcript variant X3 XM_011534799.3:c.4144= XM_011534799.3:c.4144C>T XM_011534799.3:c.4144C>G
POLE transcript variant X4 XM_011534799.2:c.4144= XM_011534799.2:c.4144C>T XM_011534799.2:c.4144C>G
POLE transcript variant X5 XM_011534799.1:c.4144= XM_011534799.1:c.4144C>T XM_011534799.1:c.4144C>G
POLE transcript variant X5 XR_941395.3:n.4171= XR_941395.3:n.4171C>T XR_941395.3:n.4171C>G
POLE transcript variant X6 XR_941395.2:n.4348= XR_941395.2:n.4348C>T XR_941395.2:n.4348C>G
POLE transcript variant X8 XR_941395.1:n.4353= XR_941395.1:n.4353C>T XR_941395.1:n.4353C>G
POLE transcript variant X4 XM_047429018.1:c.4144= XM_047429018.1:c.4144C>T XM_047429018.1:c.4144C>G
DNA polymerase epsilon catalytic subunit A NP_006222.2:p.Arg1382= NP_006222.2:p.Arg1382Cys NP_006222.2:p.Arg1382Gly
DNA polymerase epsilon catalytic subunit A isoform X1 XP_011533097.1:p.Arg1382= XP_011533097.1:p.Arg1382Cys XP_011533097.1:p.Arg1382Gly
DNA polymerase epsilon catalytic subunit A isoform X2 XP_011533099.1:p.Arg1075= XP_011533099.1:p.Arg1075Cys XP_011533099.1:p.Arg1075Gly
DNA polymerase epsilon catalytic subunit A isoform X5 XP_011533104.1:p.Arg378= XP_011533104.1:p.Arg378Cys XP_011533104.1:p.Arg378Gly
DNA polymerase epsilon catalytic subunit A isoform X3 XP_011533101.1:p.Arg1382= XP_011533101.1:p.Arg1382Cys XP_011533101.1:p.Arg1382Gly
DNA polymerase epsilon catalytic subunit A isoform X4 XP_047284974.1:p.Arg1382= XP_047284974.1:p.Arg1382Cys XP_047284974.1:p.Arg1382Gly
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#.

45 SubSNP, 9 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss7989204 Apr 21, 2003 (114)
2 ILLUMINA ss74880457 Dec 07, 2007 (129)
3 KRIBB_YJKIM ss119498079 Dec 01, 2009 (131)
4 ILLUMINA ss160744951 Dec 01, 2009 (131)
5 ILLUMINA ss173926242 Jul 04, 2010 (132)
6 BUSHMAN ss198903852 Jul 04, 2010 (132)
7 ILLUMINA ss481153936 May 04, 2012 (137)
8 ILLUMINA ss481176274 May 04, 2012 (137)
9 ILLUMINA ss482164820 Sep 08, 2015 (146)
10 ILLUMINA ss485372154 May 04, 2012 (137)
11 ILLUMINA ss537313498 Sep 08, 2015 (146)
12 ILLUMINA ss778558697 Sep 08, 2015 (146)
13 ILLUMINA ss783131683 Sep 08, 2015 (146)
14 ILLUMINA ss784088161 Sep 08, 2015 (146)
15 ILLUMINA ss832390587 Sep 08, 2015 (146)
16 ILLUMINA ss834015533 Sep 08, 2015 (146)
17 JMKIDD_LAB ss974486029 Aug 21, 2014 (142)
18 EVA_SVP ss1713371545 Apr 01, 2015 (144)
19 ILLUMINA ss1752056513 Sep 08, 2015 (146)
20 CLINVAR ss2137512114 May 05, 2017 (150)
21 ILLUMINA ss2633032602 Nov 08, 2017 (151)
22 GNOMAD ss2740285103 Nov 08, 2017 (151)
23 GNOMAD ss2749008483 Nov 08, 2017 (151)
24 GNOMAD ss2917011885 Nov 08, 2017 (151)
25 AFFY ss2984997116 Nov 08, 2017 (151)
26 ILLUMINA ss3627010289 Oct 12, 2018 (152)
27 ILLUMINA ss3631037530 Oct 12, 2018 (152)
28 ILLUMINA ss3633040831 Oct 12, 2018 (152)
29 ILLUMINA ss3633742781 Oct 12, 2018 (152)
30 ILLUMINA ss3634532953 Oct 12, 2018 (152)
31 ILLUMINA ss3635433086 Oct 12, 2018 (152)
32 ILLUMINA ss3636219232 Oct 12, 2018 (152)
33 ILLUMINA ss3637184125 Oct 12, 2018 (152)
34 ILLUMINA ss3637997260 Oct 12, 2018 (152)
35 ILLUMINA ss3640240286 Oct 12, 2018 (152)
36 ILLUMINA ss3642988158 Oct 12, 2018 (152)
37 ILLUMINA ss3653767395 Oct 12, 2018 (152)
38 ILLUMINA ss3744833721 Jul 13, 2019 (153)
39 ILLUMINA ss3772332861 Jul 13, 2019 (153)
40 KRGDB ss3928272476 Apr 27, 2020 (154)
41 TOPMED ss4938178021 Apr 26, 2021 (155)
42 TOMMO_GENOMICS ss5208935981 Apr 26, 2021 (155)
43 TOMMO_GENOMICS ss5759503677 Oct 16, 2022 (156)
44 EVA ss5936158281 Oct 16, 2022 (156)
45 EVA ss5936158282 Oct 16, 2022 (156)
46 gnomAD - Genomes NC_000012.12 - 132648934 Apr 26, 2021 (155)
47 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 9526091 (NC_000012.11:133225519:G:G 250087/250090, NC_000012.11:133225519:G:A 3/250090)
Row 9526092 (NC_000012.11:133225519:G:G 250089/250090, NC_000012.11:133225519:G:C 1/250090)

- Jul 13, 2019 (153)
48 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 9526091 (NC_000012.11:133225519:G:G 250087/250090, NC_000012.11:133225519:G:A 3/250090)
Row 9526092 (NC_000012.11:133225519:G:G 250089/250090, NC_000012.11:133225519:G:C 1/250090)

- Jul 13, 2019 (153)
49 HapMap NC_000012.12 - 132648934 Apr 27, 2020 (154)
50 KOREAN population from KRGDB NC_000012.11 - 133225520 Apr 27, 2020 (154)
51 8.3KJPN NC_000012.11 - 133225520 Apr 26, 2021 (155)
52 14KJPN NC_000012.12 - 132648934 Oct 16, 2022 (156)
53 TopMed NC_000012.12 - 132648934 Apr 26, 2021 (155)
54 ALFA NC_000012.12 - 132648934 Apr 26, 2021 (155)
55 ClinVar RCV000474418.5 Oct 16, 2022 (156)
56 ClinVar RCV000543275.6 Oct 16, 2022 (156)
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)
rs386599706 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss198903852, ss481153936, ss1713371545, ss3642988158 NC_000012.10:131735592:G:A NC_000012.12:132648933:G:A (self)
35449870, 66905288, ss481176274, ss482164820, ss485372154, ss537313498, ss778558697, ss783131683, ss784088161, ss832390587, ss834015533, ss974486029, ss1752056513, ss2633032602, ss2740285103, ss2749008483, ss2917011885, ss2984997116, ss3627010289, ss3631037530, ss3633040831, ss3633742781, ss3634532953, ss3635433086, ss3636219232, ss3637184125, ss3637997260, ss3640240286, ss3653767395, ss3744833721, ss3772332861, ss3928272476, ss5208935981, ss5936158281, ss5936158282 NC_000012.11:133225519:G:A NC_000012.12:132648933:G:A (self)
RCV000543275.6, 423979616, 937582, 93340781, 153723678, 13834241845, ss4938178021, ss5759503677 NC_000012.12:132648933:G:A NC_000012.12:132648933:G:A (self)
ss7989204, ss74880457, ss119498079, ss160744951, ss173926242 NT_024477.14:418527:G:A NC_000012.12:132648933:G:A (self)
ss2740285103, ss5936158281 NC_000012.11:133225519:G:C NC_000012.12:132648933:G:C (self)
RCV000474418.5, ss2137512114 NC_000012.12:132648933:G:C NC_000012.12:132648933:G:C (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 rs5744904

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