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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.

rs17448457

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr2:200600834 (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
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.146783 (38852/264690, TOPMED)
A=0.12633 (2405/19038, ALFA)
A=0.06689 (1121/16760, 8.3KJPN) (+ 15 more)
A=0.1172 (587/5008, 1000G)
A=0.2237 (1002/4480, Estonian)
A=0.2073 (799/3854, ALSPAC)
A=0.2136 (792/3708, TWINSUK)
A=0.1014 (297/2930, KOREAN)
A=0.0944 (173/1832, Korea1K)
A=0.189 (189/998, GoNL)
A=0.098 (77/788, PRJEB37584)
A=0.253 (152/600, NorthernSweden)
A=0.106 (35/330, HapMap)
A=0.148 (32/216, Qatari)
A=0.042 (9/212, Vietnamese)
T=0.390 (53/136, SGDP_PRJ)
A=0.28 (11/40, GENOME_DK)
T=0.3 (3/10, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
AOX1 : 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 2 NC_000002.12:g.200600834T>A
GRCh38.p13 chr 2 NC_000002.12:g.200600834T>C
GRCh37.p13 chr 2 NC_000002.11:g.201465557T>A
GRCh37.p13 chr 2 NC_000002.11:g.201465557T>C
Gene: AOX1, aldehyde oxidase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
AOX1 transcript NM_001159.4:c.436+1088T>A N/A Intron Variant
AOX1 transcript variant X1 XM_011511062.1:c.436+1088…

XM_011511062.1:c.436+1088T>A

N/A Intron Variant
AOX1 transcript variant X2 XM_017003946.1:c.436+1088…

XM_017003946.1:c.436+1088T>A

N/A Intron Variant
AOX1 transcript variant X3 XM_017003947.2:c.436+1088…

XM_017003947.2:c.436+1088T>A

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

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 19038 T=0.87367 A=0.12633, C=0.00000
European Sub 15032 T=0.84719 A=0.15281, C=0.00000
African Sub 2606 T=0.9754 A=0.0246, C=0.0000
African Others Sub 104 T=0.990 A=0.010, C=0.000
African American Sub 2502 T=0.9748 A=0.0252, C=0.0000
Asian Sub 104 T=1.000 A=0.000, C=0.000
East Asian Sub 78 T=1.00 A=0.00, C=0.00
Other Asian Sub 26 T=1.00 A=0.00, C=0.00
Latin American 1 Sub 88 T=1.00 A=0.00, C=0.00
Latin American 2 Sub 508 T=1.000 A=0.000, C=0.000
South Asian Sub 74 T=1.00 A=0.00, C=0.00
Other Sub 626 T=0.930 A=0.070, C=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
TopMed Global Study-wide 264690 T=0.853217 A=0.146783
8.3KJPN JAPANESE Study-wide 16760 T=0.93311 A=0.06689
1000Genomes Global Study-wide 5008 T=0.8828 A=0.1172
1000Genomes African Sub 1322 T=0.9440 A=0.0560
1000Genomes East Asian Sub 1008 T=0.9216 A=0.0784
1000Genomes Europe Sub 1006 T=0.7803 A=0.2197
1000Genomes South Asian Sub 978 T=0.849 A=0.151
1000Genomes American Sub 694 T=0.906 A=0.094
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.7763 A=0.2237
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.7927 A=0.2073
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.7864 A=0.2136
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.8986 A=0.1014
Korean Genome Project KOREAN Study-wide 1832 T=0.9056 A=0.0944
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.811 A=0.189
CNV burdens in cranial meningiomas Global Study-wide 788 T=0.902 A=0.098
CNV burdens in cranial meningiomas CRM Sub 788 T=0.902 A=0.098
Northern Sweden ACPOP Study-wide 600 T=0.747 A=0.253
HapMap Global Study-wide 330 T=0.894 A=0.106
HapMap African Sub 120 T=0.958 A=0.042
HapMap American Sub 120 T=0.783 A=0.217
HapMap Asian Sub 90 T=0.96 A=0.04
Qatari Global Study-wide 216 T=0.852 A=0.148
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.958 A=0.042
SGDP_PRJ Global Study-wide 136 T=0.390 A=0.610
The Danish reference pan genome Danish Study-wide 40 T=0.72 A=0.28
Siberian Global Study-wide 10 T=0.3 A=0.7
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 T= A C
GRCh38.p13 chr 2 NC_000002.12:g.200600834= NC_000002.12:g.200600834T>A NC_000002.12:g.200600834T>C
GRCh37.p13 chr 2 NC_000002.11:g.201465557= NC_000002.11:g.201465557T>A NC_000002.11:g.201465557T>C
AOX1 transcript NM_001159.3:c.436+1088= NM_001159.3:c.436+1088T>A NM_001159.3:c.436+1088T>C
AOX1 transcript NM_001159.4:c.436+1088= NM_001159.4:c.436+1088T>A NM_001159.4:c.436+1088T>C
AOX1 transcript variant X1 XM_011511062.1:c.436+1088= XM_011511062.1:c.436+1088T>A XM_011511062.1:c.436+1088T>C
AOX1 transcript variant X2 XM_017003946.1:c.436+1088= XM_017003946.1:c.436+1088T>A XM_017003946.1:c.436+1088T>C
AOX1 transcript variant X3 XM_017003947.2:c.436+1088= XM_017003947.2:c.436+1088T>A XM_017003947.2:c.436+1088T>C
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#.

76 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss24656130 Sep 20, 2004 (123)
2 ILLUMINA ss75235076 Dec 07, 2007 (129)
3 KRIBB_YJKIM ss119887197 Dec 01, 2009 (131)
4 ILLUMINA ss160444002 Dec 01, 2009 (131)
5 COMPLETE_GENOMICS ss165828434 Jul 04, 2010 (132)
6 COMPLETE_GENOMICS ss167530417 Jul 04, 2010 (132)
7 ILLUMINA ss172831553 Jul 04, 2010 (132)
8 BCM-HGSC-SUB ss205643029 Jul 04, 2010 (132)
9 1000GENOMES ss219754106 Jul 14, 2010 (132)
10 1000GENOMES ss231543917 Jul 14, 2010 (132)
11 1000GENOMES ss239015527 Jul 15, 2010 (132)
12 BL ss253812467 May 09, 2011 (134)
13 GMI ss475623981 May 04, 2012 (137)
14 ILLUMINA ss480241839 May 04, 2012 (137)
15 ILLUMINA ss480252602 May 04, 2012 (137)
16 ILLUMINA ss480992080 Sep 08, 2015 (146)
17 ILLUMINA ss484918872 May 04, 2012 (137)
18 ILLUMINA ss536969551 Sep 08, 2015 (146)
19 TISHKOFF ss556151451 Apr 25, 2013 (138)
20 SSMP ss649817951 Apr 25, 2013 (138)
21 ILLUMINA ss778342331 Sep 08, 2015 (146)
22 ILLUMINA ss782905754 Sep 08, 2015 (146)
23 ILLUMINA ss783869043 Sep 08, 2015 (146)
24 ILLUMINA ss832160617 Sep 08, 2015 (146)
25 ILLUMINA ss833796941 Sep 08, 2015 (146)
26 EVA-GONL ss977844998 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1069855052 Aug 21, 2014 (142)
28 1000GENOMES ss1301203683 Aug 21, 2014 (142)
29 EVA_GENOME_DK ss1579277389 Apr 01, 2015 (144)
30 EVA_DECODE ss1587295866 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1605558283 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1648552316 Apr 01, 2015 (144)
33 EVA_SVP ss1712522616 Apr 01, 2015 (144)
34 HAMMER_LAB ss1798187974 Sep 08, 2015 (146)
35 WEILL_CORNELL_DGM ss1921093952 Feb 12, 2016 (147)
36 GENOMED ss1968998905 Jul 19, 2016 (147)
37 JJLAB ss2021088334 Sep 14, 2016 (149)
38 USC_VALOUEV ss2149153291 Dec 20, 2016 (150)
39 HUMAN_LONGEVITY ss2238224326 Dec 20, 2016 (150)
40 TOPMED ss2404669812 Dec 20, 2016 (150)
41 GRF ss2703800289 Nov 08, 2017 (151)
42 GNOMAD ss2785063754 Nov 08, 2017 (151)
43 SWEGEN ss2991178940 Nov 08, 2017 (151)
44 ILLUMINA ss3022057852 Nov 08, 2017 (151)
45 BIOINF_KMB_FNS_UNIBA ss3024303480 Nov 08, 2017 (151)
46 TOPMED ss3335469730 Nov 08, 2017 (151)
47 CSHL ss3344692054 Nov 08, 2017 (151)
48 ILLUMINA ss3625773571 Oct 11, 2018 (152)
49 ILLUMINA ss3628261970 Oct 11, 2018 (152)
50 ILLUMINA ss3631686878 Oct 11, 2018 (152)
51 ILLUMINA ss3633230716 Oct 11, 2018 (152)
52 ILLUMINA ss3633943742 Oct 11, 2018 (152)
53 ILLUMINA ss3635629242 Oct 11, 2018 (152)
54 ILLUMINA ss3636496471 Oct 11, 2018 (152)
55 ILLUMINA ss3638312196 Oct 11, 2018 (152)
56 ILLUMINA ss3643277359 Oct 11, 2018 (152)
57 ILLUMINA ss3644765892 Oct 11, 2018 (152)
58 ILLUMINA ss3652506677 Oct 11, 2018 (152)
59 EGCUT_WGS ss3659066804 Jul 13, 2019 (153)
60 EVA_DECODE ss3705805644 Jul 13, 2019 (153)
61 ILLUMINA ss3725861814 Jul 13, 2019 (153)
62 ACPOP ss3729276133 Jul 13, 2019 (153)
63 EVA ss3757953597 Jul 13, 2019 (153)
64 PACBIO ss3784122195 Jul 13, 2019 (153)
65 PACBIO ss3789665332 Jul 13, 2019 (153)
66 PACBIO ss3794538487 Jul 13, 2019 (153)
67 KHV_HUMAN_GENOMES ss3802312899 Jul 13, 2019 (153)
68 EVA ss3827449573 Apr 25, 2020 (154)
69 EVA ss3837144377 Apr 25, 2020 (154)
70 EVA ss3842565534 Apr 25, 2020 (154)
71 SGDP_PRJ ss3854369554 Apr 25, 2020 (154)
72 KRGDB ss3900057576 Apr 25, 2020 (154)
73 KOGIC ss3949867353 Apr 25, 2020 (154)
74 EVA ss3984496210 Apr 26, 2021 (155)
75 TOPMED ss4540745130 Apr 26, 2021 (155)
76 TOMMO_GENOMICS ss5155997362 Apr 26, 2021 (155)
77 1000Genomes NC_000002.11 - 201465557 Oct 11, 2018 (152)
78 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 201465557 Oct 11, 2018 (152)
79 Genetic variation in the Estonian population NC_000002.11 - 201465557 Oct 11, 2018 (152)
80 The Danish reference pan genome NC_000002.11 - 201465557 Apr 25, 2020 (154)
81 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 87660323 (NC_000002.12:200600833:T:A 22372/139950)
Row 87660324 (NC_000002.12:200600833:T:C 2/139994)

- Apr 26, 2021 (155)
82 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 87660323 (NC_000002.12:200600833:T:A 22372/139950)
Row 87660324 (NC_000002.12:200600833:T:C 2/139994)

- Apr 26, 2021 (155)
83 Genome of the Netherlands Release 5 NC_000002.11 - 201465557 Apr 25, 2020 (154)
84 HapMap NC_000002.12 - 200600834 Apr 25, 2020 (154)
85 KOREAN population from KRGDB NC_000002.11 - 201465557 Apr 25, 2020 (154)
86 Korean Genome Project NC_000002.12 - 200600834 Apr 25, 2020 (154)
87 Northern Sweden NC_000002.11 - 201465557 Jul 13, 2019 (153)
88 CNV burdens in cranial meningiomas NC_000002.11 - 201465557 Apr 26, 2021 (155)
89 Qatari NC_000002.11 - 201465557 Apr 25, 2020 (154)
90 SGDP_PRJ NC_000002.11 - 201465557 Apr 25, 2020 (154)
91 Siberian NC_000002.11 - 201465557 Apr 25, 2020 (154)
92 8.3KJPN NC_000002.11 - 201465557 Apr 26, 2021 (155)
93 TopMed NC_000002.12 - 200600834 Apr 26, 2021 (155)
94 UK 10K study - Twins NC_000002.11 - 201465557 Oct 11, 2018 (152)
95 A Vietnamese Genetic Variation Database NC_000002.11 - 201465557 Jul 13, 2019 (153)
96 ALFA NC_000002.12 - 200600834 Apr 26, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss165828434, ss167530417, ss205643029, ss253812467, ss475623981, ss480241839, ss1587295866, ss1712522616, ss3643277359 NC_000002.10:201173801:T:A NC_000002.12:200600833:T:A (self)
12292053, 6791977, 4805052, 5442328, 2980394, 7234970, 2560998, 45546, 3135882, 6386534, 1669645, 13966669, 6791977, 1480802, ss219754106, ss231543917, ss239015527, ss480252602, ss480992080, ss484918872, ss536969551, ss556151451, ss649817951, ss778342331, ss782905754, ss783869043, ss832160617, ss833796941, ss977844998, ss1069855052, ss1301203683, ss1579277389, ss1605558283, ss1648552316, ss1798187974, ss1921093952, ss1968998905, ss2021088334, ss2149153291, ss2404669812, ss2703800289, ss2785063754, ss2991178940, ss3022057852, ss3344692054, ss3625773571, ss3628261970, ss3631686878, ss3633230716, ss3633943742, ss3635629242, ss3636496471, ss3638312196, ss3644765892, ss3652506677, ss3659066804, ss3729276133, ss3757953597, ss3784122195, ss3789665332, ss3794538487, ss3827449573, ss3837144377, ss3854369554, ss3900057576, ss3984496210, ss5155997362 NC_000002.11:201465556:T:A NC_000002.12:200600833:T:A (self)
1989394, 6245354, 215065616, 344568009, 14650764054, ss2238224326, ss3024303480, ss3335469730, ss3705805644, ss3725861814, ss3802312899, ss3842565534, ss3949867353, ss4540745130 NC_000002.12:200600833:T:A NC_000002.12:200600833:T:A (self)
ss24656130, ss75235076, ss119887197, ss160444002, ss172831553 NT_005403.17:51674974:T:A NC_000002.12:200600833:T:A (self)
ss2785063754 NC_000002.11:201465556:T:C NC_000002.12:200600833:T:C (self)
14650764054 NC_000002.12:200600833:T:C NC_000002.12:200600833:T:C
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 rs17448457

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