Skip to main page content
Accesskeys

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 Aliases 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.

rs12195525

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr6:155454846 (GRCh38.p12) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.12029 (15105/125568, TOPMED)
T=0.1096 (3438/31362, GnomAD)
T=0.1105 (1437/13006, GO-ESP) (+ 6 more)
T=0.129 (644/5008, 1000G)
T=0.097 (435/4480, Estonian)
T=0.100 (386/3854, ALSPAC)
T=0.113 (418/3708, TWINSUK)
T=0.08 (50/606, Vietnamese)
T=0.14 (82/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NOX3 : Stop Gained
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.p12 chr 6 NC_000006.12:g.155454846G>A
GRCh38.p12 chr 6 NC_000006.12:g.155454846G>T
GRCh37.p13 chr 6 NC_000006.11:g.155775980G>A
GRCh37.p13 chr 6 NC_000006.11:g.155775980G>T
NOX3 RefSeqGene NG_011995.1:g.6058C>T
NOX3 RefSeqGene NG_011995.1:g.6058C>A
Gene: NOX3, NADPH oxidase 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NOX3 transcript NM_015718.3:c.220C>T R [CGA] > * [TGA] Coding Sequence Variant
NADPH oxidase 3 NP_056533.1:p.Arg74Ter R (Arg) > * (Ter) Stop Gained
NOX3 transcript NM_015718.3:c.220C>A R [CGA] > R [AGA] Coding Sequence Variant
NADPH oxidase 3 NP_056533.1:p.Arg74= R (Arg) > R (Arg) Synonymous 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

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 125568 G=0.87971 T=0.12029
gnomAD - Genomes Global Study-wide 31362 G=0.8904 T=0.1096
gnomAD - Genomes European Sub 18888 G=0.8936 T=0.1064
gnomAD - Genomes African Sub 8696 G=0.892 T=0.108
gnomAD - Genomes East Asian Sub 1556 G=0.915 T=0.085
gnomAD - Genomes Other Sub 1086 G=0.885 T=0.115
gnomAD - Genomes American Sub 848 G=0.77 T=0.23
gnomAD - Genomes Ashkenazi Jewish Sub 288 G=0.88 T=0.12
GO Exome Sequencing Project Global Study-wide 13006 G=0.8895 T=0.1105
GO Exome Sequencing Project European American Sub 8600 G=0.888 T=0.112
GO Exome Sequencing Project African American Sub 4406 G=0.893 T=0.107
1000Genomes Global Study-wide 5008 G=0.871 T=0.129
1000Genomes African Sub 1322 G=0.893 T=0.107
1000Genomes East Asian Sub 1008 G=0.883 T=0.117
1000Genomes Europe Sub 1006 G=0.896 T=0.104
1000Genomes South Asian Sub 978 G=0.88 T=0.12
1000Genomes American Sub 694 G=0.77 T=0.23
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.903 T=0.097
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.900 T=0.100
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.887 T=0.113
A Vietnamese Genetic Variation Database Global Study-wide 606 G=0.92 T=0.08
Northern Sweden ACPOP Study-wide 600 G=0.86 T=0.14
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 T Note
GRCh38.p12 chr 6 NC_000006.12:g.15...

NC_000006.12:g.155454846=

NC_000006.12:g.15...

NC_000006.12:g.155454846G>A

NC_000006.12:g.15...

NC_000006.12:g.155454846G>T

GRCh37.p13 chr 6 NC_000006.11:g.15...

NC_000006.11:g.155775980=

NC_000006.11:g.15...

NC_000006.11:g.155775980G>A

NC_000006.11:g.15...

NC_000006.11:g.155775980G>T

NOX3 RefSeqGene NG_011995.1:g.6058= NG_011995.1:g.605...

NG_011995.1:g.6058C>T

NG_011995.1:g.605...

NG_011995.1:g.6058C>A

NOX3 transcript NM_015718.2:c.220= NM_015718.2:c.220C>T NM_015718.2:c.220C>A
NOX3 transcript NM_015718.3:c.220= NM_015718.3:c.220C>T NM_015718.3:c.220C>A
NADPH oxidase 3 NP_056533.1:p.Arg74= NP_056533.1:p.Arg...

NP_056533.1:p.Arg74Ter

NP_056533.1:p.Arg74=
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#.

94 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18375642 Feb 28, 2004 (120)
2 ABI ss44770094 Mar 13, 2006 (126)
3 APPLERA_GI ss48427173 Mar 13, 2006 (126)
4 PERLEGEN ss68997367 May 18, 2007 (127)
5 ILLUMINA ss75045527 Dec 07, 2007 (129)
6 AFFY ss76515111 Dec 07, 2007 (129)
7 BCMHGSC_JDW ss93587618 Mar 24, 2008 (129)
8 HUMANGENOME_JCVI ss98555131 Feb 05, 2009 (130)
9 1000GENOMES ss115362029 Jan 25, 2009 (130)
10 KRIBB_YJKIM ss119758358 Dec 01, 2009 (131)
11 ENSEMBL ss144168530 Dec 01, 2009 (131)
12 ENSEMBL ss144388758 Dec 01, 2009 (131)
13 SEATTLESEQ ss159713902 Dec 01, 2009 (131)
14 ILLUMINA ss160040437 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss165004352 Jul 04, 2010 (132)
16 ILLUMINA ss171921909 Jul 04, 2010 (132)
17 BUSHMAN ss202634085 Jul 04, 2010 (132)
18 1000GENOMES ss222776198 Jul 14, 2010 (132)
19 1000GENOMES ss233754311 Jul 15, 2010 (132)
20 1000GENOMES ss240755337 Jul 15, 2010 (132)
21 GMI ss279091414 May 04, 2012 (137)
22 GMI ss285533876 Apr 25, 2013 (138)
23 PJP ss293767784 May 09, 2011 (134)
24 NHLBI-ESP ss342226905 May 09, 2011 (134)
25 ILLUMINA ss479690440 May 04, 2012 (137)
26 ILLUMINA ss479696062 May 04, 2012 (137)
27 ILLUMINA ss480227355 Sep 08, 2015 (146)
28 ILLUMINA ss484643765 May 04, 2012 (137)
29 1000GENOMES ss490937484 May 04, 2012 (137)
30 CLINSEQ_SNP ss491899087 May 04, 2012 (137)
31 ILLUMINA ss536762119 Sep 08, 2015 (146)
32 TISHKOFF ss559644105 Apr 25, 2013 (138)
33 SSMP ss653987042 Apr 25, 2013 (138)
34 ILLUMINA ss778401751 Sep 08, 2015 (146)
35 ILLUMINA ss782768709 Sep 08, 2015 (146)
36 ILLUMINA ss783734934 Sep 08, 2015 (146)
37 ILLUMINA ss832021100 Sep 08, 2015 (146)
38 ILLUMINA ss833856934 Sep 08, 2015 (146)
39 JMKIDD_LAB ss974462570 Aug 21, 2014 (142)
40 EVA-GONL ss983691654 Aug 21, 2014 (142)
41 JMKIDD_LAB ss1067484203 Aug 21, 2014 (142)
42 JMKIDD_LAB ss1074178791 Aug 21, 2014 (142)
43 1000GENOMES ss1323003228 Aug 21, 2014 (142)
44 EVA_GENOME_DK ss1581969229 Apr 01, 2015 (144)
45 EVA_FINRISK ss1584049950 Apr 01, 2015 (144)
46 EVA_DECODE ss1593267881 Apr 01, 2015 (144)
47 EVA_UK10K_ALSPAC ss1617091035 Apr 01, 2015 (144)
48 EVA_UK10K_TWINSUK ss1660085068 Apr 01, 2015 (144)
49 EVA_EXAC ss1688558952 Apr 01, 2015 (144)
50 EVA_EXAC ss1688558953 Apr 01, 2015 (144)
51 EVA_MGP ss1711147563 Apr 01, 2015 (144)
52 EVA_SVP ss1712913996 Apr 01, 2015 (144)
53 ILLUMINA ss1752610881 Sep 08, 2015 (146)
54 WEILL_CORNELL_DGM ss1926934617 Feb 12, 2016 (147)
55 GENOMED ss1970567568 Jul 19, 2016 (147)
56 JJLAB ss2024132612 Sep 14, 2016 (149)
57 USC_VALOUEV ss2152324029 Dec 20, 2016 (150)
58 HUMAN_LONGEVITY ss2289911160 Dec 20, 2016 (150)
59 TOPMED ss2458599355 Dec 20, 2016 (150)
60 ILLUMINA ss2634534684 Nov 08, 2017 (151)
61 GRF ss2707961793 Nov 08, 2017 (151)
62 GNOMAD ss2736159092 Nov 08, 2017 (151)
63 GNOMAD ss2747732563 Nov 08, 2017 (151)
64 GNOMAD ss2847184574 Nov 08, 2017 (151)
65 SWEGEN ss3000239565 Nov 08, 2017 (151)
66 ILLUMINA ss3022683812 Nov 08, 2017 (151)
67 BIOINF_KMB_FNS_UNIBA ss3025856466 Nov 08, 2017 (151)
68 CSHL ss3347311074 Nov 08, 2017 (151)
69 TOPMED ss3516620263 Nov 08, 2017 (151)
70 ILLUMINA ss3629697645 Oct 12, 2018 (152)
71 ILLUMINA ss3632446687 Oct 12, 2018 (152)
72 ILLUMINA ss3633444034 Oct 12, 2018 (152)
73 ILLUMINA ss3634167895 Oct 12, 2018 (152)
74 ILLUMINA ss3635096905 Oct 12, 2018 (152)
75 ILLUMINA ss3635848185 Oct 12, 2018 (152)
76 ILLUMINA ss3636825922 Oct 12, 2018 (152)
77 ILLUMINA ss3637601080 Oct 12, 2018 (152)
78 ILLUMINA ss3638667430 Oct 12, 2018 (152)
79 ILLUMINA ss3640804206 Oct 12, 2018 (152)
80 ILLUMINA ss3643605768 Oct 12, 2018 (152)
81 OMUKHERJEE_ADBS ss3646345817 Oct 12, 2018 (152)
82 URBANLAB ss3648507778 Oct 12, 2018 (152)
83 ILLUMINA ss3653208346 Oct 12, 2018 (152)
84 EGCUT_WGS ss3668177829 Jul 13, 2019 (153)
85 EVA_DECODE ss3718636297 Jul 13, 2019 (153)
86 ILLUMINA ss3726399990 Jul 13, 2019 (153)
87 ACPOP ss3734143462 Jul 13, 2019 (153)
88 ILLUMINA ss3745396826 Jul 13, 2019 (153)
89 EVA ss3765894467 Jul 13, 2019 (153)
90 ILLUMINA ss3772890140 Jul 13, 2019 (153)
91 PACBIO ss3785668251 Jul 13, 2019 (153)
92 PACBIO ss3790987904 Jul 13, 2019 (153)
93 PACBIO ss3795867322 Jul 13, 2019 (153)
94 KHV_HUMAN_GENOMES ss3809057361 Jul 13, 2019 (153)
95 1000Genomes NC_000006.11 - 155775980 Oct 12, 2018 (152)
96 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 155775980 Oct 12, 2018 (152)
97 Genetic variation in the Estonian population NC_000006.11 - 155775980 Oct 12, 2018 (152)
98 ExAC

Submission ignored due to conflicting rows:
Row 8610901 (NC_000006.11:155775979:G:G 103827/120394, NC_000006.11:155775979:G:T 16567/120394)
Row 8610902 (NC_000006.11:155775979:G:G 120392/120394, NC_000006.11:155775979:G:A 2/120394)

- Oct 12, 2018 (152)
99 ExAC

Submission ignored due to conflicting rows:
Row 8610901 (NC_000006.11:155775979:G:G 103827/120394, NC_000006.11:155775979:G:T 16567/120394)
Row 8610902 (NC_000006.11:155775979:G:G 120392/120394, NC_000006.11:155775979:G:A 2/120394)

- Oct 12, 2018 (152)
100 gnomAD - Genomes NC_000006.11 - 155775980 Jul 13, 2019 (153)
101 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 5313283 (NC_000006.11:155775979:G:G 239683/239684, NC_000006.11:155775979:G:A 1/239684)
Row 5313284 (NC_000006.11:155775979:G:G 207567/239684, NC_000006.11:155775979:G:T 32117/239684)

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

Submission ignored due to conflicting rows:
Row 5313283 (NC_000006.11:155775979:G:G 239683/239684, NC_000006.11:155775979:G:A 1/239684)
Row 5313284 (NC_000006.11:155775979:G:G 207567/239684, NC_000006.11:155775979:G:T 32117/239684)

- Jul 13, 2019 (153)
103 GO Exome Sequencing Project NC_000006.11 - 155775980 Oct 12, 2018 (152)
104 Northern Sweden NC_000006.11 - 155775980 Jul 13, 2019 (153)
105 TopMed NC_000006.12 - 155454846 Oct 12, 2018 (152)
106 UK 10K study - Twins NC_000006.11 - 155775980 Oct 12, 2018 (152)
107 A Vietnamese Genetic Variation Database NC_000006.11 - 155775980 Jul 13, 2019 (153)
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
ss1688558953, ss2736159092 NC_000006.11:155775979:G:A NC_000006.12:155454845:G:A (self)
ss76515111, ss93587618, ss115362029, ss165004352, ss202634085, ss279091414, ss285533876, ss293767784, ss479690440, ss491899087, ss1593267881, ss1712913996, ss3643605768 NC_000006.10:155817671:G:T NC_000006.12:155454845:G:T (self)
34899921, 19461297, 13916077, 95398965, 695934, 7428327, 19461297, 4332303, ss222776198, ss233754311, ss240755337, ss342226905, ss479696062, ss480227355, ss484643765, ss490937484, ss536762119, ss559644105, ss653987042, ss778401751, ss782768709, ss783734934, ss832021100, ss833856934, ss974462570, ss983691654, ss1067484203, ss1074178791, ss1323003228, ss1581969229, ss1584049950, ss1617091035, ss1660085068, ss1688558952, ss1711147563, ss1752610881, ss1926934617, ss1970567568, ss2024132612, ss2152324029, ss2458599355, ss2634534684, ss2707961793, ss2736159092, ss2747732563, ss2847184574, ss3000239565, ss3022683812, ss3347311074, ss3629697645, ss3632446687, ss3633444034, ss3634167895, ss3635096905, ss3635848185, ss3636825922, ss3637601080, ss3638667430, ss3640804206, ss3646345817, ss3653208346, ss3668177829, ss3734143462, ss3745396826, ss3765894467, ss3772890140, ss3785668251, ss3790987904, ss3795867322 NC_000006.11:155775979:G:T NC_000006.12:155454845:G:T (self)
353723100, ss2289911160, ss3025856466, ss3516620263, ss3648507778, ss3718636297, ss3726399990, ss3809057361 NC_000006.12:155454845:G:T NC_000006.12:155454845:G:T (self)
ss18375642 NT_025741.13:59930828:G:T NC_000006.12:155454845:G:T (self)
ss44770094, ss48427173, ss68997367, ss75045527, ss98555131, ss119758358, ss144168530, ss144388758, ss159713902, ss160040437, ss171921909 NT_025741.15:59945436:G:T NC_000006.12:155454845:G: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 rs12195525

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.post308+0fe9b3b