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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.

rs10857712

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr10:133412162 (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=0.24915 (31285/125568, TOPMED)
C=0.2938 (23124/78700, PAGE_STUDY)
C=0.2316 (7254/31324, GnomAD) (+ 6 more)
C=0.287 (1438/5008, 1000G)
C=0.190 (850/4480, Estonian)
C=0.217 (838/3854, ALSPAC)
C=0.230 (854/3708, TWINSUK)
C=0.26 (154/600, NorthernSweden)
C=0.29 (61/212, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MTG1 : Intron Variant
Publications
1 citation
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 10 NC_000010.11:g.133412162T>C
GRCh37.p13 chr 10 NC_000010.10:g.135225666T>C
Gene: MTG1, mitochondrial ribosome associated GTPase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MTG1 transcript NM_138384.4: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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 T=0.75085 C=0.24915
The PAGE Study Global Study-wide 78700 T=0.7062 C=0.2938
The PAGE Study AfricanAmerican Sub 32516 T=0.7540 C=0.2460
The PAGE Study Mexican Sub 10810 T=0.6324 C=0.3676
The PAGE Study Asian Sub 8318 T=0.600 C=0.400
The PAGE Study PuertoRican Sub 7918 T=0.719 C=0.281
The PAGE Study NativeHawaiian Sub 4534 T=0.727 C=0.273
The PAGE Study Cuban Sub 4230 T=0.729 C=0.271
The PAGE Study Dominican Sub 3826 T=0.738 C=0.262
The PAGE Study CentralAmerican Sub 2450 T=0.595 C=0.405
The PAGE Study SouthAmerican Sub 1982 T=0.659 C=0.341
The PAGE Study NativeAmerican Sub 1260 T=0.752 C=0.248
The PAGE Study SouthAsian Sub 856 T=0.73 C=0.27
gnomAD - Genomes Global Study-wide 31324 T=0.7684 C=0.2316
gnomAD - Genomes European Sub 18868 T=0.7916 C=0.2084
gnomAD - Genomes African Sub 8682 T=0.748 C=0.252
gnomAD - Genomes East Asian Sub 1552 T=0.682 C=0.318
gnomAD - Genomes Other Sub 1086 T=0.749 C=0.251
gnomAD - Genomes American Sub 846 T=0.68 C=0.32
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.68 C=0.32
1000Genomes Global Study-wide 5008 T=0.713 C=0.287
1000Genomes African Sub 1322 T=0.747 C=0.253
1000Genomes East Asian Sub 1008 T=0.666 C=0.334
1000Genomes Europe Sub 1006 T=0.758 C=0.242
1000Genomes South Asian Sub 978 T=0.69 C=0.31
1000Genomes American Sub 694 T=0.68 C=0.32
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.810 C=0.190
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.783 C=0.217
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.770 C=0.230
Northern Sweden ACPOP Study-wide 600 T=0.74 C=0.26
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.71 C=0.29
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 10 NC_000010.11:g.133412162= NC_000010.11:g.13341216...

NC_000010.11:g.133412162T>C

GRCh37.p13 chr 10 NC_000010.10:g.135225666= NC_000010.10:g.13522566...

NC_000010.10:g.135225666T>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#.

109 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss15577684 Feb 27, 2004 (120)
2 CSHL-HAPMAP ss17389479 Feb 27, 2004 (120)
3 SC_SNP ss18631058 Feb 27, 2004 (120)
4 ABI ss38511429 Mar 14, 2006 (126)
5 ILLUMINA ss66667056 Dec 01, 2006 (127)
6 ILLUMINA ss66905444 Dec 01, 2006 (127)
7 ILLUMINA ss67030000 Dec 01, 2006 (127)
8 PERLEGEN ss69097784 May 17, 2007 (127)
9 ILLUMINA ss70382304 May 17, 2007 (127)
10 ILLUMINA ss70502944 May 26, 2008 (130)
11 ILLUMINA ss71029128 May 17, 2007 (127)
12 AFFY ss74841377 Aug 16, 2007 (128)
13 ILLUMINA ss75565139 Dec 06, 2007 (129)
14 KRIBB_YJKIM ss85016263 Dec 16, 2007 (130)
15 HUMANGENOME_JCVI ss97699086 Feb 06, 2009 (130)
16 BGI ss102929520 Dec 01, 2009 (131)
17 1000GENOMES ss109895664 Jan 24, 2009 (130)
18 1000GENOMES ss114069858 Jan 25, 2009 (130)
19 ILLUMINA ss121403345 Dec 01, 2009 (131)
20 ENSEMBL ss138753204 Dec 01, 2009 (131)
21 ILLUMINA ss152850194 Dec 01, 2009 (131)
22 GMI ss155787739 Dec 01, 2009 (131)
23 ILLUMINA ss159148004 Dec 01, 2009 (131)
24 ILLUMINA ss159930160 Dec 01, 2009 (131)
25 ILLUMINA ss169670811 Jul 04, 2010 (132)
26 ILLUMINA ss170653321 Jul 04, 2010 (132)
27 COMPLETE_GENOMICS ss171458278 Jul 04, 2010 (132)
28 COMPLETE_GENOMICS ss174835762 Jul 04, 2010 (132)
29 BUSHMAN ss202247568 Jul 04, 2010 (132)
30 BCM-HGSC-SUB ss207320052 Jul 04, 2010 (132)
31 1000GENOMES ss225041311 Jul 14, 2010 (132)
32 1000GENOMES ss235407515 Jul 15, 2010 (132)
33 1000GENOMES ss242070051 Jul 15, 2010 (132)
34 GMI ss280843715 May 04, 2012 (137)
35 PJP ss290971184 May 09, 2011 (134)
36 ILLUMINA ss479378484 May 04, 2012 (137)
37 ILLUMINA ss479381667 May 04, 2012 (137)
38 ILLUMINA ss479786495 Sep 08, 2015 (146)
39 ILLUMINA ss484489357 May 04, 2012 (137)
40 ILLUMINA ss536644420 Sep 08, 2015 (146)
41 TISHKOFF ss562324428 Apr 25, 2013 (138)
42 SSMP ss657632914 Apr 25, 2013 (138)
43 ILLUMINA ss778743356 Aug 21, 2014 (142)
44 ILLUMINA ss782691204 Aug 21, 2014 (142)
45 ILLUMINA ss783659459 Aug 21, 2014 (142)
46 ILLUMINA ss825351794 Apr 01, 2015 (144)
47 ILLUMINA ss831942175 Apr 01, 2015 (144)
48 ILLUMINA ss832660630 Aug 21, 2014 (142)
49 ILLUMINA ss833251319 Aug 21, 2014 (142)
50 ILLUMINA ss834202963 Aug 21, 2014 (142)
51 EVA-GONL ss988109259 Aug 21, 2014 (142)
52 JMKIDD_LAB ss1077434421 Aug 21, 2014 (142)
53 1000GENOMES ss1339755979 Aug 21, 2014 (142)
54 DDI ss1426501428 Apr 01, 2015 (144)
55 EVA_GENOME_DK ss1575463688 Apr 01, 2015 (144)
56 EVA_DECODE ss1597788285 Apr 01, 2015 (144)
57 EVA_UK10K_ALSPAC ss1625811443 Apr 01, 2015 (144)
58 EVA_UK10K_TWINSUK ss1668805476 Apr 01, 2015 (144)
59 EVA_SVP ss1713226126 Apr 01, 2015 (144)
60 ILLUMINA ss1751957660 Sep 08, 2015 (146)
61 HAMMER_LAB ss1806650578 Sep 08, 2015 (146)
62 WEILL_CORNELL_DGM ss1931467760 Feb 12, 2016 (147)
63 ILLUMINA ss1946297958 Feb 12, 2016 (147)
64 ILLUMINA ss1959312077 Feb 12, 2016 (147)
65 GENOMED ss1967268798 Jul 19, 2016 (147)
66 JJLAB ss2026474551 Sep 14, 2016 (149)
67 USC_VALOUEV ss2154757730 Dec 20, 2016 (150)
68 HUMAN_LONGEVITY ss2179504603 Dec 20, 2016 (150)
69 TOPMED ss2342617429 Dec 20, 2016 (150)
70 SYSTEMSBIOZJU ss2627706611 Nov 08, 2017 (151)
71 ILLUMINA ss2632788264 Nov 08, 2017 (151)
72 GRF ss2699022673 Nov 08, 2017 (151)
73 ILLUMINA ss2710726224 Nov 08, 2017 (151)
74 GNOMAD ss2895295784 Nov 08, 2017 (151)
75 SWEGEN ss3007431904 Nov 08, 2017 (151)
76 ILLUMINA ss3021294414 Nov 08, 2017 (151)
77 BIOINF_KMB_FNS_UNIBA ss3027029802 Nov 08, 2017 (151)
78 TOPMED ss3134790595 Nov 08, 2017 (151)
79 CSHL ss3349400757 Nov 08, 2017 (151)
80 ILLUMINA ss3625593313 Oct 12, 2018 (152)
81 ILLUMINA ss3626577242 Oct 12, 2018 (152)
82 ILLUMINA ss3630808890 Oct 12, 2018 (152)
83 ILLUMINA ss3632971864 Oct 12, 2018 (152)
84 ILLUMINA ss3633670184 Oct 12, 2018 (152)
85 ILLUMINA ss3634433527 Oct 12, 2018 (152)
86 ILLUMINA ss3635362168 Oct 12, 2018 (152)
87 ILLUMINA ss3636118750 Oct 12, 2018 (152)
88 ILLUMINA ss3637112943 Oct 12, 2018 (152)
89 ILLUMINA ss3637884778 Oct 12, 2018 (152)
90 ILLUMINA ss3638957903 Oct 12, 2018 (152)
91 ILLUMINA ss3639479310 Oct 12, 2018 (152)
92 ILLUMINA ss3640140868 Oct 12, 2018 (152)
93 ILLUMINA ss3642885166 Oct 12, 2018 (152)
94 ILLUMINA ss3644550734 Oct 12, 2018 (152)
95 URBANLAB ss3649508005 Oct 12, 2018 (152)
96 ILLUMINA ss3651654656 Oct 12, 2018 (152)
97 EGCUT_WGS ss3674850027 Jul 13, 2019 (153)
98 EVA_DECODE ss3691034955 Jul 13, 2019 (153)
99 ILLUMINA ss3725205348 Jul 13, 2019 (153)
100 ACPOP ss3737835882 Jul 13, 2019 (153)
101 ILLUMINA ss3744079130 Jul 13, 2019 (153)
102 ILLUMINA ss3744734468 Jul 13, 2019 (153)
103 EVA ss3748829887 Jul 13, 2019 (153)
104 PAGE_CC ss3771596420 Jul 13, 2019 (153)
105 ILLUMINA ss3772234670 Jul 13, 2019 (153)
106 PACBIO ss3786836651 Jul 13, 2019 (153)
107 PACBIO ss3791993045 Jul 13, 2019 (153)
108 PACBIO ss3796875300 Jul 13, 2019 (153)
109 KHV_HUMAN_GENOMES ss3814179729 Jul 13, 2019 (153)
110 1000Genomes NC_000010.10 - 135225666 Oct 12, 2018 (152)
111 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 135225666 Oct 12, 2018 (152)
112 Genetic variation in the Estonian population NC_000010.10 - 135225666 Oct 12, 2018 (152)
113 gnomAD - Genomes NC_000010.10 - 135225666 Jul 13, 2019 (153)
114 Northern Sweden NC_000010.10 - 135225666 Jul 13, 2019 (153)
115 The PAGE Study NC_000010.11 - 133412162 Jul 13, 2019 (153)
116 TopMed NC_000010.11 - 133412162 Oct 12, 2018 (152)
117 UK 10K study - Twins NC_000010.10 - 135225666 Oct 12, 2018 (152)
118 A Vietnamese Genetic Variation Database NC_000010.10 - 135225666 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)
rs52810574 Sep 21, 2007 (128)
rs61249339 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3638957903, ss3639479310 NC_000010.8:135114546:T:C NC_000010.11:133412161:T:C (self)
ss109895664, ss114069858, ss159930160, ss171458278, ss174835762, ss202247568, ss207320052, ss280843715, ss290971184, ss479378484, ss825351794, ss1597788285, ss1713226126, ss3642885166 NC_000010.9:135075655:T:C NC_000010.11:133412161:T:C (self)
52226570, 29020306, 20588275, 142649843, 11120747, 29020306, 6441196, ss225041311, ss235407515, ss242070051, ss479381667, ss479786495, ss484489357, ss536644420, ss562324428, ss657632914, ss778743356, ss782691204, ss783659459, ss831942175, ss832660630, ss833251319, ss834202963, ss988109259, ss1077434421, ss1339755979, ss1426501428, ss1575463688, ss1625811443, ss1668805476, ss1751957660, ss1806650578, ss1931467760, ss1946297958, ss1959312077, ss1967268798, ss2026474551, ss2154757730, ss2342617429, ss2627706611, ss2632788264, ss2699022673, ss2710726224, ss2895295784, ss3007431904, ss3021294414, ss3349400757, ss3625593313, ss3626577242, ss3630808890, ss3632971864, ss3633670184, ss3634433527, ss3635362168, ss3636118750, ss3637112943, ss3637884778, ss3640140868, ss3644550734, ss3651654656, ss3674850027, ss3737835882, ss3744079130, ss3744734468, ss3748829887, ss3772234670, ss3786836651, ss3791993045, ss3796875300 NC_000010.10:135225665:T:C NC_000010.11:133412161:T:C (self)
817889, 55153829, ss2179504603, ss3027029802, ss3134790595, ss3649508005, ss3691034955, ss3725205348, ss3771596420, ss3814179729 NC_000010.11:133412161:T:C NC_000010.11:133412161:T:C (self)
ss38511429, ss66667056, ss66905444, ss67030000, ss69097784, ss70382304, ss70502944, ss71029128, ss74841377, ss75565139, ss85016263, ss97699086, ss102929520, ss121403345, ss138753204, ss152850194, ss155787739, ss159148004, ss169670811, ss170653321 NT_008818.16:6459596:T:C NC_000010.11:133412161:T:C (self)
ss15577684, ss17389479, ss18631058 NT_017795.16:381244:T:C NC_000010.11:133412161: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.

1 citation for rs10857712
PMID Title Author Year Journal
24871463 GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region. Armstrong DL et al. 2014 Genes and immunity

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