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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 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.

rs72812014

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr17:878876 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.09745 (12236/125568, TOPMED)
A=0.0920 (7233/78660, PAGE_STUDY)
A=0.0953 (2987/31346, GnomAD) (+ 6 more)
A=0.076 (381/5008, 1000G)
A=0.077 (346/4480, Estonian)
A=0.073 (282/3854, ALSPAC)
A=0.087 (322/3708, TWINSUK)
A=0.07 (45/600, NorthernSweden)
A=0.04 (8/214, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NXN : 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.p12 chr 17 NC_000017.11:g.878876G>A
GRCh37.p13 chr 17 NC_000017.10:g.782116G>A
Gene: NXN, nucleoredoxin (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NXN transcript variant 1 NM_022463.5:c. N/A Intron Variant
NXN transcript variant 2 NM_001205319.1:c. N/A Genic Upstream Transcript Variant
NXN transcript variant X1 XM_005256756.4:c. N/A Intron Variant
NXN transcript variant X2 XM_005256758.3:c. N/A Intron Variant
NXN transcript variant X3 XM_017024949.1:c. 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

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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 G=0.90255 A=0.09745
The PAGE Study Global Study-wide 78660 G=0.9080 A=0.0920
The PAGE Study AfricanAmerican Sub 32490 G=0.8558 A=0.1442
The PAGE Study Mexican Sub 10808 G=0.9593 A=0.0407
The PAGE Study Asian Sub 8316 G=0.980 A=0.020
The PAGE Study PuertoRican Sub 7914 G=0.908 A=0.092
The PAGE Study NativeHawaiian Sub 4532 G=0.966 A=0.034
The PAGE Study Cuban Sub 4228 G=0.925 A=0.075
The PAGE Study Dominican Sub 3828 G=0.894 A=0.106
The PAGE Study CentralAmerican Sub 2448 G=0.945 A=0.055
The PAGE Study SouthAmerican Sub 1980 G=0.955 A=0.045
The PAGE Study NativeAmerican Sub 1260 G=0.930 A=0.070
The PAGE Study SouthAsian Sub 856 G=0.97 A=0.03
gnomAD - Genomes Global Study-wide 31346 G=0.9047 A=0.0953
gnomAD - Genomes European Sub 18878 G=0.9208 A=0.0792
gnomAD - Genomes African Sub 8690 G=0.851 A=0.149
gnomAD - Genomes East Asian Sub 1556 G=0.972 A=0.028
gnomAD - Genomes Other Sub 1084 G=0.919 A=0.081
gnomAD - Genomes American Sub 848 G=0.95 A=0.05
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=0.94 A=0.06
1000Genomes Global Study-wide 5008 G=0.924 A=0.076
1000Genomes African Sub 1322 G=0.840 A=0.160
1000Genomes East Asian Sub 1008 G=0.957 A=0.043
1000Genomes Europe Sub 1006 G=0.927 A=0.073
1000Genomes South Asian Sub 978 G=0.99 A=0.01
1000Genomes American Sub 694 G=0.94 A=0.06
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.923 A=0.077
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.927 A=0.073
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.913 A=0.087
Northern Sweden ACPOP Study-wide 600 G=0.93 A=0.07
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.96 A=0.04
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 Note
GRCh38.p12 chr 17 NC_000017.11:g.878876= NC_000017.11:g.878876G>A
GRCh37.p13 chr 17 NC_000017.10:g.782116= NC_000017.10:g.782116G>A
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#.

51 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss109583250 Feb 13, 2009 (130)
2 ILLUMINA-UK ss117970291 Dec 01, 2009 (131)
3 1000GENOMES ss227423281 Jul 14, 2010 (132)
4 1000GENOMES ss237153759 Jul 15, 2010 (132)
5 ILLUMINA ss479997413 May 04, 2012 (137)
6 ILLUMINA ss483675123 May 04, 2012 (137)
7 ILLUMINA ss533457744 Sep 08, 2015 (146)
8 TISHKOFF ss565117456 Apr 25, 2013 (138)
9 SSMP ss660900116 Apr 25, 2013 (138)
10 ILLUMINA ss780639617 Sep 08, 2015 (146)
11 ILLUMINA ss781121056 Sep 08, 2015 (146)
12 ILLUMINA ss836133913 Sep 08, 2015 (146)
13 EVA-GONL ss992839553 Aug 21, 2014 (142)
14 JMKIDD_LAB ss1080875161 Aug 21, 2014 (142)
15 1000GENOMES ss1357594055 Aug 21, 2014 (142)
16 DDI ss1427951633 Apr 01, 2015 (144)
17 EVA_GENOME_DK ss1578055021 Apr 01, 2015 (144)
18 EVA_UK10K_ALSPAC ss1635131859 Apr 01, 2015 (144)
19 EVA_UK10K_TWINSUK ss1678125892 Apr 01, 2015 (144)
20 EVA_DECODE ss1696879860 Apr 01, 2015 (144)
21 HAMMER_LAB ss1808666089 Sep 08, 2015 (146)
22 WEILL_CORNELL_DGM ss1936284371 Feb 12, 2016 (147)
23 ILLUMINA ss1959712746 Feb 12, 2016 (147)
24 JJLAB ss2028930961 Sep 14, 2016 (149)
25 USC_VALOUEV ss2157373806 Dec 20, 2016 (150)
26 HUMAN_LONGEVITY ss2214882987 Dec 20, 2016 (150)
27 TOPMED ss2379713108 Dec 20, 2016 (150)
28 ILLUMINA ss2633364486 Nov 08, 2017 (151)
29 GNOMAD ss2946803434 Nov 08, 2017 (151)
30 AFFY ss2985080899 Nov 08, 2017 (151)
31 AFFY ss2985718925 Nov 08, 2017 (151)
32 SWEGEN ss3015057997 Nov 08, 2017 (151)
33 ILLUMINA ss3021743322 Nov 08, 2017 (151)
34 BIOINF_KMB_FNS_UNIBA ss3028283120 Nov 08, 2017 (151)
35 TOPMED ss3255257880 Nov 08, 2017 (151)
36 CSHL ss3351612647 Nov 08, 2017 (151)
37 ILLUMINA ss3627605088 Oct 12, 2018 (152)
38 ILLUMINA ss3631347781 Oct 12, 2018 (152)
39 ILLUMINA ss3641978365 Oct 12, 2018 (152)
40 ILLUMINA ss3652155781 Oct 12, 2018 (152)
41 ILLUMINA ss3653853005 Oct 12, 2018 (152)
42 EGCUT_WGS ss3682030799 Jul 13, 2019 (153)
43 EVA_DECODE ss3699922726 Jul 13, 2019 (153)
44 ILLUMINA ss3725592437 Jul 13, 2019 (153)
45 ACPOP ss3741800074 Jul 13, 2019 (153)
46 EVA ss3754353511 Jul 13, 2019 (153)
47 PAGE_CC ss3771904376 Jul 13, 2019 (153)
48 PACBIO ss3788126231 Jul 13, 2019 (153)
49 PACBIO ss3793097416 Jul 13, 2019 (153)
50 PACBIO ss3797982894 Jul 13, 2019 (153)
51 KHV_HUMAN_GENOMES ss3819623511 Jul 13, 2019 (153)
52 1000Genomes NC_000017.10 - 782116 Oct 12, 2018 (152)
53 The Avon Longitudinal Study of Parents and Children NC_000017.10 - 782116 Oct 12, 2018 (152)
54 Genetic variation in the Estonian population NC_000017.10 - 782116 Oct 12, 2018 (152)
55 gnomAD - Genomes NC_000017.10 - 782116 Jul 13, 2019 (153)
56 Northern Sweden NC_000017.10 - 782116 Jul 13, 2019 (153)
57 The PAGE Study NC_000017.11 - 878876 Jul 13, 2019 (153)
58 TopMed NC_000017.11 - 878876 Oct 12, 2018 (152)
59 UK 10K study - Twins NC_000017.10 - 782116 Oct 12, 2018 (152)
60 A Vietnamese Genetic Variation Database NC_000017.10 - 782116 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).

Associated ID History Updated (Build)
rs386431641 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss109583250, ss117970291, ss483675123, ss1696879860 NC_000017.9:728865:G:A NC_000017.11:878875:G:A (self)
70796292, 39269579, 27769047, 193184739, 15084939, 39269579, 8700715, ss227423281, ss237153759, ss479997413, ss533457744, ss565117456, ss660900116, ss780639617, ss781121056, ss836133913, ss992839553, ss1080875161, ss1357594055, ss1427951633, ss1578055021, ss1635131859, ss1678125892, ss1808666089, ss1936284371, ss1959712746, ss2028930961, ss2157373806, ss2379713108, ss2633364486, ss2946803434, ss2985080899, ss2985718925, ss3015057997, ss3021743322, ss3351612647, ss3627605088, ss3631347781, ss3641978365, ss3652155781, ss3653853005, ss3682030799, ss3741800074, ss3754353511, ss3788126231, ss3793097416, ss3797982894 NC_000017.10:782115:G:A NC_000017.11:878875:G:A (self)
1125845, 151258709, ss2214882987, ss3028283120, ss3255257880, ss3699922726, ss3725592437, ss3771904376, ss3819623511 NC_000017.11:878875:G:A NC_000017.11:878875:G:A (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 rs72812014

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