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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.

rs10074959

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr5:104872312 (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=0.30338 (38095/125568, TOPMED)
A=0.3302 (25990/78702, PAGE_STUDY)
A=0.3013 (9434/31308, GnomAD) (+ 6 more)
A=0.289 (1449/5008, 1000G)
A=0.236 (1058/4480, Estonian)
A=0.228 (879/3854, ALSPAC)
A=0.240 (891/3708, TWINSUK)
A=0.30 (183/600, NorthernSweden)
A=0.32 (68/214, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 5 NC_000005.10:g.104872312G>A
GRCh37.p13 chr 5 NC_000005.9:g.104208013G>A
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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=0.69662 A=0.30338
The PAGE Study Global Study-wide 78702 G=0.6698 A=0.3302
The PAGE Study AfricanAmerican Sub 32516 G=0.5535 A=0.4465
The PAGE Study Mexican Sub 10810 G=0.8145 A=0.1855
The PAGE Study Asian Sub 8318 G=0.724 A=0.276
The PAGE Study PuertoRican Sub 7918 G=0.747 A=0.253
The PAGE Study NativeHawaiian Sub 4534 G=0.710 A=0.290
The PAGE Study Cuban Sub 4230 G=0.728 A=0.272
The PAGE Study Dominican Sub 3828 G=0.646 A=0.354
The PAGE Study CentralAmerican Sub 2450 G=0.794 A=0.206
The PAGE Study SouthAmerican Sub 1982 G=0.800 A=0.200
The PAGE Study NativeAmerican Sub 1260 G=0.752 A=0.248
The PAGE Study SouthAsian Sub 856 G=0.84 A=0.16
gnomAD - Genomes Global Study-wide 31308 G=0.6987 A=0.3013
gnomAD - Genomes European Sub 18866 G=0.7577 A=0.2423
gnomAD - Genomes African Sub 8670 G=0.549 A=0.451
gnomAD - Genomes East Asian Sub 1554 G=0.732 A=0.268
gnomAD - Genomes Other Sub 1082 G=0.739 A=0.261
gnomAD - Genomes American Sub 846 G=0.78 A=0.22
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=0.76 A=0.24
1000Genomes Global Study-wide 5008 G=0.711 A=0.289
1000Genomes African Sub 1322 G=0.495 A=0.505
1000Genomes East Asian Sub 1008 G=0.725 A=0.275
1000Genomes Europe Sub 1006 G=0.754 A=0.246
1000Genomes South Asian Sub 978 G=0.88 A=0.12
1000Genomes American Sub 694 G=0.79 A=0.21
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.764 A=0.236
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.772 A=0.228
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.760 A=0.240
Northern Sweden ACPOP Study-wide 600 G=0.69 A=0.30
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.68 A=0.32
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 5 NC_000005.10:g.104872312= NC_000005.10:g.10487231...

NC_000005.10:g.104872312G>A

GRCh37.p13 chr 5 NC_000005.9:g.104208013= NC_000005.9:g.104208013G>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#.

94 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss13927952 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss17861941 Feb 27, 2004 (120)
3 ILLUMINA ss66941922 Nov 29, 2006 (127)
4 ILLUMINA ss70984384 May 16, 2007 (127)
5 ILLUMINA ss75391447 Dec 06, 2007 (129)
6 HGSV ss84379242 Dec 16, 2007 (130)
7 1000GENOMES ss109279595 Jan 23, 2009 (130)
8 1000GENOMES ss112302808 Jan 25, 2009 (130)
9 ILLUMINA-UK ss116741695 Feb 14, 2009 (130)
10 KRIBB_YJKIM ss119612521 Dec 01, 2009 (131)
11 GMI ss155827998 Dec 01, 2009 (131)
12 ILLUMINA ss159859691 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss162509617 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss165628690 Jul 04, 2010 (132)
15 ILLUMINA ss169622008 Jul 04, 2010 (132)
16 BUSHMAN ss200623243 Jul 04, 2010 (132)
17 BCM-HGSC-SUB ss206921928 Jul 04, 2010 (132)
18 1000GENOMES ss221852789 Jul 14, 2010 (132)
19 1000GENOMES ss233070131 Jul 14, 2010 (132)
20 1000GENOMES ss240212261 Jul 15, 2010 (132)
21 BL ss253677271 May 09, 2011 (134)
22 GMI ss278410556 May 04, 2012 (137)
23 PJP ss293424821 May 09, 2011 (134)
24 ILLUMINA ss479177865 May 04, 2012 (137)
25 ILLUMINA ss479179937 May 04, 2012 (137)
26 ILLUMINA ss479505237 Sep 08, 2015 (146)
27 ILLUMINA ss484389998 May 04, 2012 (137)
28 ILLUMINA ss536572939 Sep 08, 2015 (146)
29 TISHKOFF ss558589719 Apr 25, 2013 (138)
30 SSMP ss652475387 Apr 25, 2013 (138)
31 ILLUMINA ss778346223 Sep 08, 2015 (146)
32 ILLUMINA ss782641337 Sep 08, 2015 (146)
33 ILLUMINA ss783610771 Sep 08, 2015 (146)
34 ILLUMINA ss831891532 Sep 08, 2015 (146)
35 ILLUMINA ss833800881 Sep 08, 2015 (146)
36 EVA-GONL ss981909278 Aug 21, 2014 (142)
37 JMKIDD_LAB ss1072883241 Aug 21, 2014 (142)
38 1000GENOMES ss1316402651 Aug 21, 2014 (142)
39 HAMMER_LAB ss1397422022 Sep 08, 2015 (146)
40 DDI ss1430444008 Apr 01, 2015 (144)
41 EVA_GENOME_DK ss1581267474 Apr 01, 2015 (144)
42 EVA_DECODE ss1591429479 Apr 01, 2015 (144)
43 EVA_UK10K_ALSPAC ss1613577591 Apr 01, 2015 (144)
44 EVA_UK10K_TWINSUK ss1656571624 Apr 01, 2015 (144)
45 EVA_SVP ss1712786478 Apr 01, 2015 (144)
46 ILLUMINA ss1752540217 Sep 08, 2015 (146)
47 HAMMER_LAB ss1803957901 Sep 08, 2015 (146)
48 WEILL_CORNELL_DGM ss1925161856 Feb 12, 2016 (147)
49 ILLUMINA ss1946151180 Feb 12, 2016 (147)
50 ILLUMINA ss1958809339 Feb 12, 2016 (147)
51 JJLAB ss2023187105 Sep 14, 2016 (149)
52 USC_VALOUEV ss2151344743 Dec 20, 2016 (150)
53 HUMAN_LONGEVITY ss2276439226 Dec 20, 2016 (150)
54 TOPMED ss2444716658 Dec 20, 2016 (150)
55 SYSTEMSBIOZJU ss2626087528 Nov 08, 2017 (151)
56 ILLUMINA ss2634316599 Nov 08, 2017 (151)
57 GRF ss2706902057 Nov 08, 2017 (151)
58 ILLUMINA ss2711044863 Nov 08, 2017 (151)
59 GNOMAD ss2828457036 Nov 08, 2017 (151)
60 SWEGEN ss2997471128 Nov 08, 2017 (151)
61 ILLUMINA ss3022513816 Nov 08, 2017 (151)
62 BIOINF_KMB_FNS_UNIBA ss3025377202 Nov 08, 2017 (151)
63 CSHL ss3346536001 Nov 08, 2017 (151)
64 TOPMED ss3473335196 Nov 08, 2017 (151)
65 ILLUMINA ss3625879565 Oct 12, 2018 (152)
66 ILLUMINA ss3629300871 Oct 12, 2018 (152)
67 ILLUMINA ss3632241769 Oct 12, 2018 (152)
68 ILLUMINA ss3633383943 Oct 12, 2018 (152)
69 ILLUMINA ss3634104895 Oct 12, 2018 (152)
70 ILLUMINA ss3635014486 Oct 12, 2018 (152)
71 ILLUMINA ss3635786747 Oct 12, 2018 (152)
72 ILLUMINA ss3636727024 Oct 12, 2018 (152)
73 ILLUMINA ss3637539385 Oct 12, 2018 (152)
74 ILLUMINA ss3638570522 Oct 12, 2018 (152)
75 ILLUMINA ss3640721780 Oct 12, 2018 (152)
76 ILLUMINA ss3641182876 Oct 12, 2018 (152)
77 ILLUMINA ss3641479822 Oct 12, 2018 (152)
78 ILLUMINA ss3643515308 Oct 12, 2018 (152)
79 ILLUMINA ss3644884154 Oct 12, 2018 (152)
80 ILLUMINA ss3653013616 Oct 12, 2018 (152)
81 ILLUMINA ss3654102476 Oct 12, 2018 (152)
82 EGCUT_WGS ss3665362471 Jul 13, 2019 (153)
83 EVA_DECODE ss3715314194 Jul 13, 2019 (153)
84 ILLUMINA ss3726255794 Jul 13, 2019 (153)
85 ACPOP ss3732642212 Jul 13, 2019 (153)
86 ILLUMINA ss3744257188 Jul 13, 2019 (153)
87 ILLUMINA ss3745314712 Jul 13, 2019 (153)
88 EVA ss3763818499 Jul 13, 2019 (153)
89 PAGE_CC ss3771220382 Jul 13, 2019 (153)
90 ILLUMINA ss3772808763 Jul 13, 2019 (153)
91 PACBIO ss3785198788 Jul 13, 2019 (153)
92 PACBIO ss3790590575 Jul 13, 2019 (153)
93 PACBIO ss3795467303 Jul 13, 2019 (153)
94 KHV_HUMAN_GENOMES ss3806989779 Jul 13, 2019 (153)
95 1000Genomes NC_000005.9 - 104208013 Oct 12, 2018 (152)
96 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 104208013 Oct 12, 2018 (152)
97 Genetic variation in the Estonian population NC_000005.9 - 104208013 Oct 12, 2018 (152)
98 gnomAD - Genomes NC_000005.9 - 104208013 Jul 13, 2019 (153)
99 Northern Sweden NC_000005.9 - 104208013 Jul 13, 2019 (153)
100 The PAGE Study NC_000005.10 - 104872312 Jul 13, 2019 (153)
101 TopMed NC_000005.10 - 104872312 Oct 12, 2018 (152)
102 UK 10K study - Twins NC_000005.9 - 104208013 Oct 12, 2018 (152)
103 A Vietnamese Genetic Variation Database NC_000005.9 - 104208013 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)
rs61421303 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss84379242, ss109279595, ss112302808, ss116741695, ss162509617, ss165628690, ss200623243, ss206921928, ss253677271, ss278410556, ss293424821, ss479177865, ss1397422022, ss1591429479, ss1712786478, ss3643515308 NC_000005.8:104235911:G:A NC_000005.10:104872311:G:A (self)
28052863, 15598564, 11100719, 76726557, 5927077, 15598564, 3461426, ss221852789, ss233070131, ss240212261, ss479179937, ss479505237, ss484389998, ss536572939, ss558589719, ss652475387, ss778346223, ss782641337, ss783610771, ss831891532, ss833800881, ss981909278, ss1072883241, ss1316402651, ss1430444008, ss1581267474, ss1613577591, ss1656571624, ss1752540217, ss1803957901, ss1925161856, ss1946151180, ss1958809339, ss2023187105, ss2151344743, ss2444716658, ss2626087528, ss2634316599, ss2706902057, ss2711044863, ss2828457036, ss2997471128, ss3022513816, ss3346536001, ss3625879565, ss3629300871, ss3632241769, ss3633383943, ss3634104895, ss3635014486, ss3635786747, ss3636727024, ss3637539385, ss3638570522, ss3640721780, ss3641182876, ss3641479822, ss3644884154, ss3653013616, ss3654102476, ss3665362471, ss3732642212, ss3744257188, ss3745314712, ss3763818499, ss3772808763, ss3785198788, ss3790590575, ss3795467303 NC_000005.9:104208012:G:A NC_000005.10:104872311:G:A (self)
441851, 318249143, ss2276439226, ss3025377202, ss3473335196, ss3715314194, ss3726255794, ss3771220382, ss3806989779 NC_000005.10:104872311:G:A NC_000005.10:104872311:G:A (self)
ss13927952, ss17861941 NT_034772.5:6623025:G:A NC_000005.10:104872311:G:A (self)
ss66941922, ss70984384, ss75391447, ss119612521, ss155827998, ss159859691, ss169622008 NT_034772.6:12521884:G:A NC_000005.10:104872311: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 rs10074959

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