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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.

rs190907564

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr8:94250483 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000321 (85/264690, TOPMED)
A=0.000088 (22/251290, GnomAD_exome)
A=0.000328 (46/140262, GnomAD) (+ 7 more)
A=0.000048 (6/124458, ALFA)
A=0.000157 (19/121338, ExAC)
A=0.00052 (41/78612, PAGE_STUDY)
A=0.00054 (7/13006, GO-ESP)
A=0.0008 (5/6404, 1000G_30x)
A=0.0008 (4/5008, 1000G)
A=0.002 (1/534, MGP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GEM : Missense Variant
Publications
0 citations
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 140870 G=0.999929 A=0.000071
European Sub 114166 G=1.000000 A=0.000000
African Sub 8338 G=0.9989 A=0.0011
African Others Sub 300 G=1.000 A=0.000
African American Sub 8038 G=0.9989 A=0.0011
Asian Sub 3132 G=1.0000 A=0.0000
East Asian Sub 1914 G=1.0000 A=0.0000
Other Asian Sub 1218 G=1.0000 A=0.0000
Latin American 1 Sub 506 G=0.998 A=0.002
Latin American 2 Sub 650 G=1.000 A=0.000
South Asian Sub 104 G=1.000 A=0.000
Other Sub 13974 G=1.00000 A=0.00000


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=0.999679 A=0.000321
gnomAD - Exomes Global Study-wide 251290 G=0.999912 A=0.000088
gnomAD - Exomes European Sub 135230 G=0.999985 A=0.000015
gnomAD - Exomes Asian Sub 49010 G=0.99992 A=0.00008
gnomAD - Exomes American Sub 34590 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16254 G=0.99902 A=0.00098
gnomAD - Exomes Ashkenazi Jewish Sub 10072 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6134 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140262 G=0.999672 A=0.000328
gnomAD - Genomes European Sub 75958 G=0.99997 A=0.00003
gnomAD - Genomes African Sub 42044 G=0.99905 A=0.00095
gnomAD - Genomes American Sub 13658 G=0.99993 A=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3128 G=0.9994 A=0.0006
gnomAD - Genomes Other Sub 2150 G=0.9995 A=0.0005
Allele Frequency Aggregator Total Global 124458 G=0.999952 A=0.000048
Allele Frequency Aggregator European Sub 104026 G=1.000000 A=0.000000
Allele Frequency Aggregator Other Sub 12540 G=1.00000 A=0.00000
Allele Frequency Aggregator African Sub 3500 G=0.9986 A=0.0014
Allele Frequency Aggregator Asian Sub 3132 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 650 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 506 G=0.998 A=0.002
Allele Frequency Aggregator South Asian Sub 104 G=1.000 A=0.000
ExAC Global Study-wide 121338 G=0.999843 A=0.000157
ExAC Europe Sub 73322 G=1.00000 A=0.00000
ExAC Asian Sub 25160 G=0.99984 A=0.00016
ExAC American Sub 11564 G=1.00000 A=0.00000
ExAC African Sub 10388 G=0.99856 A=0.00144
ExAC Other Sub 904 G=1.000 A=0.000
The PAGE Study Global Study-wide 78612 G=0.99948 A=0.00052
The PAGE Study AfricanAmerican Sub 32468 G=0.99883 A=0.00117
The PAGE Study Mexican Sub 10802 G=1.00000 A=0.00000
The PAGE Study Asian Sub 8308 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7910 G=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4528 G=1.0000 A=0.0000
The PAGE Study Cuban Sub 4226 G=1.0000 A=0.0000
The PAGE Study Dominican Sub 3826 G=0.9992 A=0.0008
The PAGE Study CentralAmerican Sub 2450 G=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 G=1.0000 A=0.0000
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 852 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13006 G=0.99946 A=0.00054
GO Exome Sequencing Project European American Sub 8600 G=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4406 G=0.9984 A=0.0016
1000Genomes_30x Global Study-wide 6404 G=0.9992 A=0.0008
1000Genomes_30x African Sub 1786 G=0.9972 A=0.0028
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9992 A=0.0008
1000Genomes African Sub 1322 G=0.9970 A=0.0030
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.998 A=0.002
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 8 NC_000008.11:g.94250483G>A
GRCh37.p13 chr 8 NC_000008.10:g.95262711G>A
Gene: GEM, GTP binding protein overexpressed in skeletal muscle (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GEM transcript variant 1 NM_005261.4:c.718C>T R [CGC] > C [TGC] Coding Sequence Variant
GTP-binding protein GEM NP_005252.1:p.Arg240Cys R (Arg) > C (Cys) Missense Variant
GEM transcript variant 2 NM_181702.3:c.718C>T R [CGC] > C [TGC] Coding Sequence Variant
GTP-binding protein GEM NP_859053.1:p.Arg240Cys R (Arg) > C (Cys) Missense Variant
GEM transcript variant X1 XM_017013315.2:c.*269= N/A 3 Prime UTR Variant
GEM transcript variant X2 XM_047421686.1:c.*269= 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

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
GRCh38.p14 chr 8 NC_000008.11:g.94250483= NC_000008.11:g.94250483G>A
GRCh37.p13 chr 8 NC_000008.10:g.95262711= NC_000008.10:g.95262711G>A
GEM transcript variant 1 NM_005261.4:c.718= NM_005261.4:c.718C>T
GEM transcript variant 1 NM_005261.3:c.718= NM_005261.3:c.718C>T
GEM transcript variant 2 NM_181702.3:c.718= NM_181702.3:c.718C>T
GEM transcript variant 2 NM_181702.2:c.718= NM_181702.2:c.718C>T
GEM transcript variant X1 XM_017013315.2:c.*269= XM_017013315.2:c.*269C>T
GEM transcript variant X1 XM_017013315.1:c.*269= XM_017013315.1:c.*269C>T
GEM transcript variant X2 XM_047421686.1:c.*269= XM_047421686.1:c.*269C>T
GTP-binding protein GEM NP_005252.1:p.Arg240= NP_005252.1:p.Arg240Cys
GTP-binding protein GEM NP_859053.1:p.Arg240= NP_859053.1:p.Arg240Cys
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#.

40 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss460621870 Sep 17, 2011 (135)
2 1000GENOMES ss490967498 May 04, 2012 (137)
3 EXOME_CHIP ss491415148 May 04, 2012 (137)
4 NHLBI-ESP ss712852020 Apr 25, 2013 (138)
5 ILLUMINA ss780871311 Sep 08, 2015 (146)
6 ILLUMINA ss783556401 Sep 08, 2015 (146)
7 1000GENOMES ss1331001793 Aug 21, 2014 (142)
8 EVA_EXAC ss1689254577 Apr 01, 2015 (144)
9 EVA_MGP ss1711205642 Apr 01, 2015 (144)
10 ILLUMINA ss1752746945 Sep 08, 2015 (146)
11 ILLUMINA ss1917830106 Feb 12, 2016 (147)
12 ILLUMINA ss1946241878 Feb 12, 2016 (147)
13 ILLUMINA ss1959127767 Feb 12, 2016 (147)
14 HUMAN_LONGEVITY ss2305510871 Dec 20, 2016 (150)
15 GNOMAD ss2737249993 Nov 08, 2017 (151)
16 GNOMAD ss2748076220 Nov 08, 2017 (151)
17 GNOMAD ss2870083504 Nov 08, 2017 (151)
18 AFFY ss2985443749 Nov 08, 2017 (151)
19 ILLUMINA ss3022864714 Nov 08, 2017 (151)
20 ILLUMINA ss3630112885 Oct 12, 2018 (152)
21 ILLUMINA ss3635181379 Oct 12, 2018 (152)
22 ILLUMINA ss3640888671 Oct 12, 2018 (152)
23 ILLUMINA ss3644975126 Oct 12, 2018 (152)
24 ILLUMINA ss3653409786 Oct 12, 2018 (152)
25 ILLUMINA ss3654206627 Oct 12, 2018 (152)
26 ILLUMINA ss3726555152 Jul 13, 2019 (153)
27 ILLUMINA ss3744581714 Jul 13, 2019 (153)
28 ILLUMINA ss3745481278 Jul 13, 2019 (153)
29 PAGE_CC ss3771456041 Jul 13, 2019 (153)
30 ILLUMINA ss3772973634 Jul 13, 2019 (153)
31 EVA ss3824381408 Apr 26, 2020 (154)
32 TOPMED ss4796244614 Apr 26, 2021 (155)
33 1000G_HIGH_COVERAGE ss5278144167 Oct 16, 2022 (156)
34 EVA ss5382989488 Oct 16, 2022 (156)
35 HUGCELL_USP ss5474602075 Oct 16, 2022 (156)
36 1000G_HIGH_COVERAGE ss5569055263 Oct 16, 2022 (156)
37 SANFORD_IMAGENETICS ss5645958435 Oct 16, 2022 (156)
38 EVA ss5848183566 Oct 16, 2022 (156)
39 EVA ss5890111508 Oct 16, 2022 (156)
40 EVA ss5975188982 Oct 16, 2022 (156)
41 1000Genomes NC_000008.10 - 95262711 Oct 12, 2018 (152)
42 1000Genomes_30x NC_000008.11 - 94250483 Oct 16, 2022 (156)
43 ExAC NC_000008.10 - 95262711 Oct 12, 2018 (152)
44 gnomAD - Genomes NC_000008.11 - 94250483 Apr 26, 2021 (155)
45 gnomAD - Exomes NC_000008.10 - 95262711 Jul 13, 2019 (153)
46 GO Exome Sequencing Project NC_000008.10 - 95262711 Oct 12, 2018 (152)
47 Medical Genome Project healthy controls from Spanish population NC_000008.10 - 95262711 Apr 26, 2020 (154)
48 The PAGE Study NC_000008.11 - 94250483 Jul 13, 2019 (153)
49 TopMed NC_000008.11 - 94250483 Apr 26, 2021 (155)
50 ALFA NC_000008.11 - 94250483 Apr 26, 2021 (155)
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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
43167181, 9359985, 6422711, 839244, 321402, ss460621870, ss490967498, ss491415148, ss712852020, ss780871311, ss783556401, ss1331001793, ss1689254577, ss1711205642, ss1752746945, ss1917830106, ss1946241878, ss1959127767, ss2737249993, ss2748076220, ss2870083504, ss2985443749, ss3022864714, ss3630112885, ss3635181379, ss3640888671, ss3644975126, ss3653409786, ss3654206627, ss3744581714, ss3745481278, ss3772973634, ss3824381408, ss5382989488, ss5645958435, ss5848183566, ss5975188982 NC_000008.10:95262710:G:A NC_000008.11:94250482:G:A (self)
56581198, 304468073, 677510, 633622174, 11017764613, ss2305510871, ss3726555152, ss3771456041, ss4796244614, ss5278144167, ss5474602075, ss5569055263, ss5890111508 NC_000008.11:94250482:G:A NC_000008.11:94250482: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 rs190907564

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