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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.

rs10282

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr19:19508508 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.43881 (55101/125568, TOPMED)
C=0.4118 (12901/31326, GnomAD)
C=0.474 (2372/5008, 1000G) (+ 5 more)
C=0.314 (1405/4480, Estonian)
C=0.343 (1321/3854, ALSPAC)
C=0.340 (1259/3708, TWINSUK)
C=0.32 (191/600, NorthernSweden)
C=0.40 (84/210, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GATAD2A : 3 Prime UTR 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 19 NC_000019.10:g.19508508T>C
GRCh37.p13 chr 19 NC_000019.9:g.19619317T>C
Gene: GATAD2A, GATA zinc finger domain containing 2A (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GATAD2A transcript variant 1 NM_001300946.2:c.*3034= N/A 3 Prime UTR Variant
GATAD2A transcript variant 2 NM_017660.4:c.*3034= N/A 3 Prime UTR Variant
GATAD2A transcript variant 3 NM_001359631.1:c.*3034= N/A 3 Prime UTR Variant
GATAD2A transcript variant X1 XM_017026901.1:c.*3034= N/A 3 Prime UTR Variant
GATAD2A transcript variant X2 XM_017026902.1:c.*3034= N/A 3 Prime UTR Variant
GATAD2A transcript variant X3 XM_017026903.1:c.*3034= N/A 3 Prime UTR Variant
GATAD2A transcript variant X4 XM_017026904.1:c.*3034= N/A 3 Prime UTR Variant
GATAD2A transcript variant X6 XM_017026907.1:c.*3034= N/A 3 Prime UTR Variant
GATAD2A transcript variant X9 XM_017026910.1:c.*3034= N/A 3 Prime UTR Variant
GATAD2A transcript variant X5 XM_011528105.2:c.*3034= N/A 3 Prime UTR Variant
GATAD2A transcript variant X7 XM_024451558.1:c.*3034= N/A 3 Prime UTR Variant
GATAD2A transcript variant X8 XM_024451559.1:c.*3034= N/A 3 Prime UTR Variant
GATAD2A transcript variant X10 XM_024451560.1:c.*3034= N/A 3 Prime UTR Variant
GATAD2A transcript variant X11 XM_017026905.2:c.*3034= N/A 3 Prime UTR 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 T=0.56119 C=0.43881
gnomAD - Genomes Global Study-wide 31326 T=0.5882 C=0.4118
gnomAD - Genomes European Sub 18866 T=0.6784 C=0.3216
gnomAD - Genomes African Sub 8686 T=0.373 C=0.627
gnomAD - Genomes East Asian Sub 1556 T=0.684 C=0.316
gnomAD - Genomes Other Sub 1080 T=0.614 C=0.386
gnomAD - Genomes American Sub 848 T=0.56 C=0.44
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.62 C=0.38
1000Genomes Global Study-wide 5008 T=0.526 C=0.474
1000Genomes African Sub 1322 T=0.344 C=0.656
1000Genomes East Asian Sub 1008 T=0.681 C=0.319
1000Genomes Europe Sub 1006 T=0.675 C=0.325
1000Genomes South Asian Sub 978 T=0.47 C=0.53
1000Genomes American Sub 694 T=0.52 C=0.48
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.686 C=0.314
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.657 C=0.343
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.660 C=0.340
Northern Sweden ACPOP Study-wide 600 T=0.68 C=0.32
A Vietnamese Genetic Variation Database Global Study-wide 210 T=0.60 C=0.40
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= C Note
GRCh38.p12 chr 19 NC_000019.10:g.19508508= NC_000019.10:g.19508508T>C
GRCh37.p13 chr 19 NC_000019.9:g.19619317= NC_000019.9:g.19619317T>C
GATAD2A transcript variant 2 NM_017660.4:c.*3034= NM_017660.4:c.*3034T>C
GATAD2A transcript variant 2 NM_017660.3:c.*3034= NM_017660.3:c.*3034T>C
GATAD2A transcript variant 1 NM_001300946.2:c.*3034= NM_001300946.2:c.*3034T>C
GATAD2A transcript variant X11 XM_017026905.2:c.*3034= XM_017026905.2:c.*3034T>C
GATAD2A transcript variant X5 XM_011528105.2:c.*3034= XM_011528105.2:c.*3034T>C
GATAD2A transcript variant X7 XM_024451558.1:c.*3034= XM_024451558.1:c.*3034T>C
GATAD2A transcript variant X8 XM_024451559.1:c.*3034= XM_024451559.1:c.*3034T>C
GATAD2A transcript variant X6 XM_017026907.1:c.*3034= XM_017026907.1:c.*3034T>C
GATAD2A transcript variant X3 XM_017026903.1:c.*3034= XM_017026903.1:c.*3034T>C
GATAD2A transcript variant X4 XM_017026904.1:c.*3034= XM_017026904.1:c.*3034T>C
GATAD2A transcript variant X10 XM_024451560.1:c.*3034= XM_024451560.1:c.*3034T>C
GATAD2A transcript variant 3 NM_001359631.1:c.*3034= NM_001359631.1:c.*3034T>C
GATAD2A transcript variant X2 XM_017026902.1:c.*3034= XM_017026902.1:c.*3034T>C
GATAD2A transcript variant X9 XM_017026910.1:c.*3034= XM_017026910.1:c.*3034T>C
GATAD2A transcript variant X1 XM_017026901.1:c.*3034= XM_017026901.1:c.*3034T>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#.

89 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 CGAP-GAI ss12432 Sep 19, 2000 (52)
2 LEE ss1532194 Oct 04, 2000 (86)
3 LEE ss4396259 May 29, 2002 (106)
4 LEE ss4421269 May 29, 2002 (106)
5 BCM_SSAHASNP ss14718856 Dec 05, 2003 (119)
6 SC_SNP ss15406806 Feb 27, 2004 (120)
7 CSHL-HAPMAP ss16806650 Feb 27, 2004 (120)
8 ABI ss44193086 Mar 13, 2006 (126)
9 ILLUMINA ss75224068 Dec 07, 2007 (129)
10 HGSV ss85189345 Dec 15, 2007 (130)
11 HUMANGENOME_JCVI ss96294702 Feb 05, 2009 (130)
12 1000GENOMES ss111164893 Jan 25, 2009 (130)
13 ILLUMINA-UK ss117658615 Feb 14, 2009 (130)
14 KRIBB_YJKIM ss119338707 Dec 01, 2009 (131)
15 ENSEMBL ss132736582 Dec 01, 2009 (131)
16 ILLUMINA ss159886667 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss167924132 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss169272279 Jul 04, 2010 (132)
19 ILLUMINA ss169981459 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss171580583 Jul 04, 2010 (132)
21 BUSHMAN ss203703389 Jul 04, 2010 (132)
22 BCM-HGSC-SUB ss208453614 Jul 04, 2010 (132)
23 1000GENOMES ss211945423 Jul 14, 2010 (132)
24 1000GENOMES ss228070848 Jul 14, 2010 (132)
25 1000GENOMES ss237624578 Jul 15, 2010 (132)
26 1000GENOMES ss243841747 Jul 15, 2010 (132)
27 BL ss255544769 May 09, 2011 (134)
28 GMI ss283147972 May 04, 2012 (137)
29 PJP ss292223123 May 09, 2011 (134)
30 ILLUMINA ss410827721 Sep 17, 2011 (135)
31 ILLUMINA ss479248387 May 04, 2012 (137)
32 ILLUMINA ss479251143 May 04, 2012 (137)
33 ILLUMINA ss479612581 Sep 08, 2015 (146)
34 ILLUMINA ss484424904 May 04, 2012 (137)
35 ILLUMINA ss536598683 Sep 08, 2015 (146)
36 TISHKOFF ss565895863 Apr 25, 2013 (138)
37 SSMP ss661752846 Apr 25, 2013 (138)
38 ILLUMINA ss778729482 Sep 08, 2015 (146)
39 ILLUMINA ss782658904 Sep 08, 2015 (146)
40 ILLUMINA ss783627976 Sep 08, 2015 (146)
41 ILLUMINA ss831909376 Sep 08, 2015 (146)
42 ILLUMINA ss834188956 Sep 08, 2015 (146)
43 EVA-GONL ss994157374 Aug 21, 2014 (142)
44 JMKIDD_LAB ss1081802975 Aug 21, 2014 (142)
45 1000GENOMES ss1362625190 Aug 21, 2014 (142)
46 DDI ss1428356453 Apr 01, 2015 (144)
47 EVA_GENOME_DK ss1578583374 Apr 01, 2015 (144)
48 EVA_UK10K_ALSPAC ss1637694692 Apr 01, 2015 (144)
49 EVA_UK10K_TWINSUK ss1680688725 Apr 01, 2015 (144)
50 EVA_SVP ss1713654880 Apr 01, 2015 (144)
51 ILLUMINA ss1752277888 Sep 08, 2015 (146)
52 HAMMER_LAB ss1809242181 Sep 08, 2015 (146)
53 WEILL_CORNELL_DGM ss1937644815 Feb 12, 2016 (147)
54 GENOMED ss1968616290 Jul 19, 2016 (147)
55 JJLAB ss2029596124 Sep 14, 2016 (149)
56 USC_VALOUEV ss2158125070 Dec 20, 2016 (150)
57 HUMAN_LONGEVITY ss2224840554 Dec 20, 2016 (150)
58 TOPMED ss2390332789 Dec 20, 2016 (150)
59 ILLUMINA ss2633525946 Nov 08, 2017 (151)
60 GRF ss2702729169 Nov 08, 2017 (151)
61 ILLUMINA ss2710879012 Nov 08, 2017 (151)
62 GNOMAD ss2961269760 Nov 08, 2017 (151)
63 SWEGEN ss3017220975 Nov 08, 2017 (151)
64 BIOINF_KMB_FNS_UNIBA ss3028630344 Nov 08, 2017 (151)
65 TOPMED ss3289722980 Nov 08, 2017 (151)
66 CSHL ss3352231652 Nov 08, 2017 (151)
67 ILLUMINA ss3627905704 Oct 12, 2018 (152)
68 ILLUMINA ss3631498340 Oct 12, 2018 (152)
69 ILLUMINA ss3633176712 Oct 12, 2018 (152)
70 ILLUMINA ss3633886801 Oct 12, 2018 (152)
71 ILLUMINA ss3634729364 Oct 12, 2018 (152)
72 ILLUMINA ss3635573714 Oct 12, 2018 (152)
73 ILLUMINA ss3636416925 Oct 12, 2018 (152)
74 ILLUMINA ss3637325430 Oct 12, 2018 (152)
75 ILLUMINA ss3638220673 Oct 12, 2018 (152)
76 ILLUMINA ss3640436672 Oct 12, 2018 (152)
77 ILLUMINA ss3643194106 Oct 12, 2018 (152)
78 OMUKHERJEE_ADBS ss3646532904 Oct 12, 2018 (152)
79 URBANLAB ss3650882590 Oct 12, 2018 (152)
80 EGCUT_WGS ss3684041464 Jul 13, 2019 (153)
81 EVA_DECODE ss3702491459 Jul 13, 2019 (153)
82 ACPOP ss3742916782 Jul 13, 2019 (153)
83 ILLUMINA ss3745029400 Jul 13, 2019 (153)
84 EVA ss3755893768 Jul 13, 2019 (153)
85 ILLUMINA ss3772526588 Jul 13, 2019 (153)
86 PACBIO ss3788489419 Jul 13, 2019 (153)
87 PACBIO ss3793405730 Jul 13, 2019 (153)
88 PACBIO ss3798292506 Jul 13, 2019 (153)
89 KHV_HUMAN_GENOMES ss3821147334 Jul 13, 2019 (153)
90 1000Genomes NC_000019.9 - 19619317 Oct 12, 2018 (152)
91 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 19619317 Oct 12, 2018 (152)
92 Genetic variation in the Estonian population NC_000019.9 - 19619317 Oct 12, 2018 (152)
93 gnomAD - Genomes NC_000019.9 - 19619317 Jul 13, 2019 (153)
94 Northern Sweden NC_000019.9 - 19619317 Jul 13, 2019 (153)
95 TopMed NC_000019.10 - 19508508 Oct 12, 2018 (152)
96 UK 10K study - Twins NC_000019.9 - 19619317 Oct 12, 2018 (152)
97 A Vietnamese Genetic Variation Database NC_000019.9 - 19619317 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)
rs3170494 Jul 03, 2002 (106)
rs59155874 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85189345, ss111164893, ss117658615, ss167924132, ss169272279, ss171580583, ss203703389, ss208453614, ss211945423, ss255544769, ss283147972, ss292223123, ss479248387, ss1713654880, ss3643194106 NC_000019.8:19480316:T:C NC_000019.10:19508507:T:C (self)
76013230, 42106858, 29779712, 207509271, 16201647, 42106858, 9303911, ss228070848, ss237624578, ss243841747, ss479251143, ss479612581, ss484424904, ss536598683, ss565895863, ss661752846, ss778729482, ss782658904, ss783627976, ss831909376, ss834188956, ss994157374, ss1081802975, ss1362625190, ss1428356453, ss1578583374, ss1637694692, ss1680688725, ss1752277888, ss1809242181, ss1937644815, ss1968616290, ss2029596124, ss2158125070, ss2390332789, ss2633525946, ss2702729169, ss2710879012, ss2961269760, ss3017220975, ss3352231652, ss3627905704, ss3631498340, ss3633176712, ss3633886801, ss3634729364, ss3635573714, ss3636416925, ss3637325430, ss3638220673, ss3640436672, ss3646532904, ss3684041464, ss3742916782, ss3745029400, ss3755893768, ss3772526588, ss3788489419, ss3793405730, ss3798292506 NC_000019.9:19619316:T:C NC_000019.10:19508507:T:C (self)
178344918, ss2224840554, ss3028630344, ss3289722980, ss3650882590, ss3702491459, ss3821147334 NC_000019.10:19508507:T:C NC_000019.10:19508507:T:C (self)
ss14718856, ss15406806, ss16806650 NT_011295.10:10882118:T:C NC_000019.10:19508507:T:C (self)
ss12432, ss1532194, ss4396259, ss4421269, ss44193086, ss75224068, ss96294702, ss119338707, ss132736582, ss159886667, ss169981459, ss410827721 NT_011295.11:10882118:T:C NC_000019.10:19508507:T: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 rs10282

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