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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 HGVS 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.

rs2890849

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:174730759 (GRCh38.p14) 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>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.205134 (54297/264690, TOPMED)
G=0.207621 (29057/139952, GnomAD)
G=0.02424 (685/28258, 14KJPN) (+ 15 more)
G=0.02333 (391/16760, 8.3KJPN)
G=0.2109 (1830/8676, ALFA)
G=0.1771 (1134/6404, 1000G_30x)
G=0.1701 (852/5008, 1000G)
G=0.1295 (499/3854, ALSPAC)
G=0.1365 (506/3708, TWINSUK)
G=0.0147 (43/2930, KOREAN)
G=0.151 (151/998, GoNL)
G=0.103 (62/600, NorthernSweden)
G=0.090 (49/542, SGDP_PRJ)
G=0.189 (101/534, MGP)
G=0.167 (36/216, Qatari)
G=0.005 (1/210, Vietnamese)
G=0.07 (4/54, Siberian)
G=0.15 (6/40, GENOME_DK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MSX2 : 3 Prime UTR Variant
Publications
1 citation
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 8676 G=0.2109 C=0.7891, T=0.0000
European Sub 7460 G=0.1614 C=0.8386, T=0.0000
African Sub 948 G=0.580 C=0.420, T=0.000
African Others Sub 46 G=0.65 C=0.35, T=0.00
African American Sub 902 G=0.576 C=0.424, T=0.000
Asian Sub 4 G=0.0 C=1.0, T=0.0
East Asian Sub 2 G=0.0 C=1.0, T=0.0
Other Asian Sub 2 G=0.0 C=1.0, T=0.0
Latin American 1 Sub 12 G=1.00 C=0.00, T=0.00
Latin American 2 Sub 2 G=1.0 C=0.0, T=0.0
South Asian Sub 4 G=0.0 C=1.0, T=0.0
Other Sub 246 G=0.252 C=0.748, T=0.000


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 264690 G=0.205134 C=0.794866
gnomAD - Genomes Global Study-wide 139952 G=0.207621 C=0.792379
gnomAD - Genomes European Sub 75878 G=0.14401 C=0.85599
gnomAD - Genomes African Sub 41824 G=0.36740 C=0.63260
gnomAD - Genomes American Sub 13650 G=0.13231 C=0.86769
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.1598 C=0.8402
gnomAD - Genomes East Asian Sub 3134 G=0.0150 C=0.9850
gnomAD - Genomes Other Sub 2144 G=0.1772 C=0.8228
14KJPN JAPANESE Study-wide 28258 G=0.02424 C=0.97576
8.3KJPN JAPANESE Study-wide 16760 G=0.02333 C=0.97667
Allele Frequency Aggregator Total Global 8676 G=0.2109 C=0.7891, T=0.0000
Allele Frequency Aggregator European Sub 7460 G=0.1614 C=0.8386, T=0.0000
Allele Frequency Aggregator African Sub 948 G=0.580 C=0.420, T=0.000
Allele Frequency Aggregator Other Sub 246 G=0.252 C=0.748, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 12 G=1.00 C=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 4 G=0.0 C=1.0, T=0.0
Allele Frequency Aggregator Asian Sub 4 G=0.0 C=1.0, T=0.0
Allele Frequency Aggregator Latin American 2 Sub 2 G=1.0 C=0.0, T=0.0
1000Genomes_30x Global Study-wide 6404 G=0.1771 C=0.8229
1000Genomes_30x African Sub 1786 G=0.4043 C=0.5957
1000Genomes_30x Europe Sub 1266 G=0.1619 C=0.8381
1000Genomes_30x South Asian Sub 1202 G=0.0441 C=0.9559
1000Genomes_30x East Asian Sub 1170 G=0.0162 C=0.9838
1000Genomes_30x American Sub 980 G=0.138 C=0.862
1000Genomes Global Study-wide 5008 G=0.1701 C=0.8299
1000Genomes African Sub 1322 G=0.4017 C=0.5983
1000Genomes East Asian Sub 1008 G=0.0149 C=0.9851
1000Genomes Europe Sub 1006 G=0.1600 C=0.8400
1000Genomes South Asian Sub 978 G=0.049 C=0.951
1000Genomes American Sub 694 G=0.140 C=0.860
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.1295 C=0.8705
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.1365 C=0.8635
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.0147 C=0.9853
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.151 C=0.849
Northern Sweden ACPOP Study-wide 600 G=0.103 C=0.897
SGDP_PRJ Global Study-wide 542 G=0.090 C=0.910
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.189 C=0.811
Qatari Global Study-wide 216 G=0.167 C=0.833
A Vietnamese Genetic Variation Database Global Study-wide 210 G=0.005 C=0.995
Siberian Global Study-wide 54 G=0.07 C=0.93
The Danish reference pan genome Danish Study-wide 40 G=0.15 C=0.85
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.p14 chr 5 NC_000005.10:g.174730759G>C
GRCh38.p14 chr 5 NC_000005.10:g.174730759G>T
GRCh37.p13 chr 5 NC_000005.9:g.174157762G>C
GRCh37.p13 chr 5 NC_000005.9:g.174157762G>T
MSX2 RefSeqGene NG_008124.1:g.11188G>C
MSX2 RefSeqGene NG_008124.1:g.11188G>T
Gene: MSX2, msh homeobox 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MSX2 transcript variant 1 NM_002449.5:c.*1176= N/A 3 Prime UTR Variant
MSX2 transcript variant 2 NM_001363626.2:c.*1604= 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.

Allele: C (allele ID: 298907 )
ClinVar Accession Disease Names Clinical Significance
RCV000359850.3 Craniosynostosis 2 Benign
RCV000393366.3 Parietal foramina 1 Benign
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= C T
GRCh38.p14 chr 5 NC_000005.10:g.174730759= NC_000005.10:g.174730759G>C NC_000005.10:g.174730759G>T
GRCh37.p13 chr 5 NC_000005.9:g.174157762= NC_000005.9:g.174157762G>C NC_000005.9:g.174157762G>T
MSX2 RefSeqGene NG_008124.1:g.11188= NG_008124.1:g.11188G>C NG_008124.1:g.11188G>T
MSX2 transcript variant 1 NM_002449.5:c.*1176= NM_002449.5:c.*1176G>C NM_002449.5:c.*1176G>T
MSX2 transcript variant 1 NM_002449.4:c.*1176= NM_002449.4:c.*1176G>C NM_002449.4:c.*1176G>T
MSX2 transcript variant 2 NM_001363626.2:c.*1604= NM_001363626.2:c.*1604G>C NM_001363626.2:c.*1604G>T
MSX2 transcript variant 2 NM_001363626.1:c.*1604= NM_001363626.1:c.*1604G>C NM_001363626.1:c.*1604G>T
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#.

78 SubSNP, 18 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss4083457 Nov 05, 2001 (101)
2 SC_JCM ss5872026 Feb 20, 2003 (111)
3 SBOYD ss6313886 Feb 20, 2003 (111)
4 BCM_SSAHASNP ss10250127 Jul 11, 2003 (116)
5 WI_SSAHASNP ss14680142 Dec 05, 2003 (119)
6 SC_SNP ss14848714 Dec 05, 2003 (119)
7 CSHL-HAPMAP ss19646030 Feb 27, 2004 (120)
8 SSAHASNP ss22331826 Apr 05, 2004 (121)
9 ABI ss42580825 Mar 14, 2006 (126)
10 HGSV ss80679328 Dec 15, 2007 (130)
11 HUMANGENOME_JCVI ss98789809 Feb 06, 2009 (130)
12 BGI ss105970888 Feb 06, 2009 (130)
13 1000GENOMES ss109647009 Jan 24, 2009 (130)
14 1000GENOMES ss113701897 Jan 25, 2009 (130)
15 ILLUMINA-UK ss116917064 Feb 14, 2009 (130)
16 GMI ss156365657 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss166295352 Jul 04, 2010 (132)
18 BUSHMAN ss201242558 Jul 04, 2010 (132)
19 BCM-HGSC-SUB ss206936362 Jul 04, 2010 (132)
20 1000GENOMES ss222132413 Jul 14, 2010 (132)
21 1000GENOMES ss233267918 Jul 14, 2010 (132)
22 BL ss253959612 May 09, 2011 (134)
23 GMI ss278597052 May 04, 2012 (137)
24 GMI ss285313909 Apr 25, 2013 (138)
25 PJP ss293526124 May 09, 2011 (134)
26 TISHKOFF ss558908447 Apr 25, 2013 (138)
27 SSMP ss652818218 Apr 25, 2013 (138)
28 EVA-GONL ss982440595 Aug 21, 2014 (142)
29 JMKIDD_LAB ss1073279126 Aug 21, 2014 (142)
30 1000GENOMES ss1318435431 Aug 21, 2014 (142)
31 DDI ss1430591645 Apr 01, 2015 (144)
32 EVA_GENOME_DK ss1581474030 Apr 01, 2015 (144)
33 EVA_DECODE ss1591984481 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1614671280 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1657665313 Apr 01, 2015 (144)
36 EVA_MGP ss1711106872 Apr 01, 2015 (144)
37 HAMMER_LAB ss1804214411 Sep 08, 2015 (146)
38 WEILL_CORNELL_DGM ss1925690877 Feb 12, 2016 (147)
39 GENOMED ss1970278193 Jul 19, 2016 (147)
40 JJLAB ss2023460523 Sep 14, 2016 (149)
41 USC_VALOUEV ss2151620267 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2626218034 Nov 08, 2017 (151)
43 GRF ss2707198021 Nov 08, 2017 (151)
44 GNOMAD ss2834254685 Nov 08, 2017 (151)
45 SWEGEN ss2998282442 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3025513186 Nov 08, 2017 (151)
47 CSHL ss3346765144 Nov 08, 2017 (151)
48 OMUKHERJEE_ADBS ss3646328111 Oct 12, 2018 (152)
49 URBANLAB ss3648233513 Oct 12, 2018 (152)
50 EVA_DECODE ss3716305300 Jul 13, 2019 (153)
51 ACPOP ss3733079737 Jul 13, 2019 (153)
52 EVA ss3764442234 Jul 13, 2019 (153)
53 PACBIO ss3785331638 Jul 13, 2019 (153)
54 PACBIO ss3790702009 Jul 13, 2019 (153)
55 PACBIO ss3795579175 Jul 13, 2019 (153)
56 KHV_HUMAN_GENOMES ss3807602960 Jul 13, 2019 (153)
57 EVA ss3825686232 Apr 26, 2020 (154)
58 EVA ss3829657380 Apr 26, 2020 (154)
59 EVA ss3838302542 Apr 26, 2020 (154)
60 EVA ss3843746641 Apr 26, 2020 (154)
61 SGDP_PRJ ss3863610962 Apr 26, 2020 (154)
62 KRGDB ss3910327183 Apr 26, 2020 (154)
63 FSA-LAB ss3984323950 Apr 26, 2021 (155)
64 FSA-LAB ss3984323951 Apr 26, 2021 (155)
65 EVA ss3986032735 Apr 26, 2021 (155)
66 TOPMED ss4689308747 Apr 26, 2021 (155)
67 TOMMO_GENOMICS ss5175523244 Apr 26, 2021 (155)
68 1000G_HIGH_COVERAGE ss5266911598 Oct 13, 2022 (156)
69 EVA ss5362939812 Oct 13, 2022 (156)
70 HUGCELL_USP ss5464771625 Oct 13, 2022 (156)
71 1000G_HIGH_COVERAGE ss5552112616 Oct 13, 2022 (156)
72 SANFORD_IMAGENETICS ss5639486649 Oct 13, 2022 (156)
73 TOMMO_GENOMICS ss5712999177 Oct 13, 2022 (156)
74 YY_MCH ss5807026598 Oct 13, 2022 (156)
75 EVA ss5836059771 Oct 13, 2022 (156)
76 EVA ss5855143020 Oct 13, 2022 (156)
77 EVA ss5897565598 Oct 13, 2022 (156)
78 EVA ss5967987789 Oct 13, 2022 (156)
79 1000Genomes NC_000005.9 - 174157762 Oct 12, 2018 (152)
80 1000Genomes_30x NC_000005.10 - 174730759 Oct 13, 2022 (156)
81 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 174157762 Oct 12, 2018 (152)
82 The Danish reference pan genome NC_000005.9 - 174157762 Apr 26, 2020 (154)
83 gnomAD - Genomes NC_000005.10 - 174730759 Apr 26, 2021 (155)
84 Genome of the Netherlands Release 5 NC_000005.9 - 174157762 Apr 26, 2020 (154)
85 KOREAN population from KRGDB NC_000005.9 - 174157762 Apr 26, 2020 (154)
86 Medical Genome Project healthy controls from Spanish population NC_000005.9 - 174157762 Apr 26, 2020 (154)
87 Northern Sweden NC_000005.9 - 174157762 Jul 13, 2019 (153)
88 Qatari NC_000005.9 - 174157762 Apr 26, 2020 (154)
89 SGDP_PRJ NC_000005.9 - 174157762 Apr 26, 2020 (154)
90 Siberian NC_000005.9 - 174157762 Apr 26, 2020 (154)
91 8.3KJPN NC_000005.9 - 174157762 Apr 26, 2021 (155)
92 14KJPN NC_000005.10 - 174730759 Oct 13, 2022 (156)
93 TopMed NC_000005.10 - 174730759 Apr 26, 2021 (155)
94 UK 10K study - Twins NC_000005.9 - 174157762 Oct 12, 2018 (152)
95 A Vietnamese Genetic Variation Database NC_000005.9 - 174157762 Jul 13, 2019 (153)
96 ALFA NC_000005.10 - 174730759 Apr 26, 2021 (155)
97 ClinVar RCV000359850.3 Oct 13, 2022 (156)
98 ClinVar RCV000393366.3 Oct 13, 2022 (156)
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)
rs60162358 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss80679328, ss109647009, ss113701897, ss116917064, ss166295352, ss201242558, ss206936362, ss253959612, ss278597052, ss285313909, ss293526124, ss1591984481 NC_000005.8:174090367:G:C NC_000005.10:174730758:G:C (self)
30157148, 16793176, 7638969, 7452137, 17504577, 222632, 6364602, 7732807, 15627942, 4136621, 33492551, 16793176, 3720564, ss222132413, ss233267918, ss558908447, ss652818218, ss982440595, ss1073279126, ss1318435431, ss1430591645, ss1581474030, ss1614671280, ss1657665313, ss1711106872, ss1804214411, ss1925690877, ss1970278193, ss2023460523, ss2151620267, ss2626218034, ss2707198021, ss2834254685, ss2998282442, ss3346765144, ss3646328111, ss3733079737, ss3764442234, ss3785331638, ss3790702009, ss3795579175, ss3825686232, ss3829657380, ss3838302542, ss3863610962, ss3910327183, ss3984323950, ss3984323951, ss3986032735, ss5175523244, ss5362939812, ss5639486649, ss5836059771, ss5967987789 NC_000005.9:174157761:G:C NC_000005.10:174730758:G:C (self)
RCV000359850.3, RCV000393366.3, 39638551, 213271947, 46836281, 526686304, 3511185723, ss3025513186, ss3648233513, ss3716305300, ss3807602960, ss3843746641, ss4689308747, ss5266911598, ss5464771625, ss5552112616, ss5712999177, ss5807026598, ss5855143020, ss5897565598 NC_000005.10:174730758:G:C NC_000005.10:174730758:G:C (self)
ss10250127, ss14680142, ss14848714, ss19646030, ss22331826 NT_023133.11:18967347:G:C NC_000005.10:174730758:G:C (self)
ss4083457, ss5872026, ss6313886, ss42580825, ss98789809, ss105970888, ss156365657 NT_023133.13:18969034:G:C NC_000005.10:174730758:G:C (self)
3511185723 NC_000005.10:174730758:G:T NC_000005.10:174730758: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.

1 citation for rs2890849
PMID Title Author Year Journal
23940558 Targeted re-sequencing identified rs3106189 at the 5' UTR of TAPBP and rs1052918 at the 3' UTR of TCF3 to be associated with the overall survival of colorectal cancer patients. Shao J et al. 2013 PloS one
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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.post761+d5e8e07