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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.

rs2500239

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr1:241068075 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.02766 (3473/125568, TOPMED)
A=0.0251 (777/30934, GnomAD)
A=0.026 (132/5008, 1000G) (+ 4 more)
A=0.000 (0/3854, ALSPAC)
A=0.000 (0/3708, TWINSUK)
A=0.00 (0/600, NorthernSweden)
A=0.00 (0/210, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RGS7 : Intron 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 1 NC_000001.11:g.241068075A>G
GRCh37.p13 chr 1 NC_000001.10:g.241231375A>G
Gene: RGS7, regulator of G protein signaling 7 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
RGS7 transcript variant 2 NM_001282773.2:c. N/A Intron Variant
RGS7 transcript variant 3 NM_001282775.2:c. N/A Intron Variant
RGS7 transcript variant 4 NM_001282778.2:c. N/A Intron Variant
RGS7 transcript variant 5 NM_001350113.1:c. N/A Intron Variant
RGS7 transcript variant 6 NM_001350114.1:c. N/A Intron Variant
RGS7 transcript variant 7 NM_001350115.1:c. N/A Intron Variant
RGS7 transcript variant 8 NM_001350116.1:c. N/A Intron Variant
RGS7 transcript variant 9 NM_001364886.1:c. N/A Intron Variant
RGS7 transcript variant 1 NM_002924.6:c. N/A Intron Variant
RGS7 transcript variant X4 XM_006711800.4:c. N/A Intron Variant
RGS7 transcript variant X5 XM_011544246.3:c. N/A Intron Variant
RGS7 transcript variant X6 XM_011544247.3:c. N/A Intron Variant
RGS7 transcript variant X2 XM_017002001.2:c. N/A Intron Variant
RGS7 transcript variant X3 XM_017002002.2:c. N/A Intron Variant
RGS7 transcript variant X7 XM_017002003.2:c. N/A Intron Variant
RGS7 transcript variant X8 XM_017002004.2:c. N/A Intron Variant
RGS7 transcript variant X9 XM_017002005.2:c. N/A Intron Variant
RGS7 transcript variant X10 XM_017002009.1:c. N/A Intron Variant
RGS7 transcript variant X11 XM_017002011.2:c. N/A Genic Upstream Transcript Variant
RGS7 transcript variant X12 XM_017002012.2:c. N/A Genic Upstream Transcript Variant
RGS7 transcript variant X13 XM_017002013.1:c. N/A Genic Upstream Transcript 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 A=0.02766 G=0.97234
gnomAD - Genomes Global Study-wide 30934 A=0.0251 G=0.9749
gnomAD - Genomes European Sub 18612 A=0.0002 G=0.9998
gnomAD - Genomes African Sub 8586 A=0.089 G=0.911
gnomAD - Genomes East Asian Sub 1554 A=0.000 G=1.000
gnomAD - Genomes Other Sub 1072 A=0.003 G=0.997
gnomAD - Genomes American Sub 822 A=0.00 G=1.00
gnomAD - Genomes Ashkenazi Jewish Sub 288 A=0.00 G=1.00
1000Genomes Global Study-wide 5008 A=0.026 G=0.974
1000Genomes African Sub 1322 A=0.095 G=0.905
1000Genomes East Asian Sub 1008 A=0.000 G=1.000
1000Genomes Europe Sub 1006 A=0.001 G=0.999
1000Genomes South Asian Sub 978 A=0.00 G=1.00
1000Genomes American Sub 694 A=0.01 G=0.99
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.000 G=1.000
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.000 G=1.000
Northern Sweden ACPOP Study-wide 600 A=0.00 G=1.00
A Vietnamese Genetic Variation Database Global Study-wide 210 A=0.00 G=1.00
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 A= G Note
GRCh38.p12 chr 1 NC_000001.11:g.241068075= NC_000001.11:g.24106807...

NC_000001.11:g.241068075A>G

GRCh37.p13 chr 1 NC_000001.10:g.241231375= NC_000001.10:g.24123137...

NC_000001.10:g.241231375A>G

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#.

54 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3506912 Sep 28, 2001 (100)
2 BCM_SSAHASNP ss9856549 Jul 11, 2003 (116)
3 SC_SNP ss13017565 Dec 05, 2003 (119)
4 BCM_SSAHASNP ss14154749 Dec 05, 2003 (119)
5 SSAHASNP ss20593473 Apr 05, 2004 (121)
6 HGSV ss77431980 Dec 06, 2007 (129)
7 HGSV ss78304215 Dec 06, 2007 (129)
8 BCMHGSC_JDW ss88032372 Mar 23, 2008 (129)
9 HUMANGENOME_JCVI ss98015828 Feb 03, 2009 (130)
10 BGI ss106644363 Feb 03, 2009 (130)
11 1000GENOMES ss109091792 Jan 23, 2009 (130)
12 1000GENOMES ss112037513 Jan 25, 2009 (130)
13 ILLUMINA-UK ss119271450 Feb 15, 2009 (130)
14 ENSEMBL ss138184995 Dec 01, 2009 (131)
15 ENSEMBL ss142896541 Dec 01, 2009 (131)
16 GMI ss156503251 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss165935373 Jul 04, 2010 (132)
18 BCM-HGSC-SUB ss205062064 Jul 04, 2010 (132)
19 1000GENOMES ss218978458 Jul 14, 2010 (132)
20 1000GENOMES ss230974871 Jul 14, 2010 (132)
21 1000GENOMES ss238574525 Jul 15, 2010 (132)
22 GMI ss276289263 May 04, 2012 (137)
23 GMI ss284260760 Apr 25, 2013 (138)
24 PJP ss290770889 May 09, 2011 (134)
25 SSMP ss648828078 Apr 25, 2013 (138)
26 JMKIDD_LAB ss1068743452 Aug 21, 2014 (142)
27 1000GENOMES ss1295339232 Aug 21, 2014 (142)
28 DDI ss1426167641 Apr 01, 2015 (144)
29 EVA_GENOME_DK ss1574799680 Apr 01, 2015 (144)
30 EVA_DECODE ss1585735983 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1602509991 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1645504024 Apr 01, 2015 (144)
33 HAMMER_LAB ss1795999062 Sep 08, 2015 (146)
34 WEILL_CORNELL_DGM ss1919553396 Feb 12, 2016 (147)
35 GENOMED ss1967018147 Jul 19, 2016 (147)
36 JJLAB ss2020304339 Sep 14, 2016 (149)
37 USC_VALOUEV ss2148342292 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2171504650 Dec 20, 2016 (150)
39 TOPMED ss2334157284 Dec 20, 2016 (150)
40 SYSTEMSBIOZJU ss2624665574 Nov 08, 2017 (151)
41 GRF ss2698345809 Nov 08, 2017 (151)
42 GNOMAD ss2768149236 Nov 08, 2017 (151)
43 SWEGEN ss2988737977 Nov 08, 2017 (151)
44 BIOINF_KMB_FNS_UNIBA ss3023914534 Nov 08, 2017 (151)
45 TOPMED ss3107816399 Nov 08, 2017 (151)
46 CSHL ss3343996635 Nov 08, 2017 (151)
47 URBANLAB ss3646926893 Oct 11, 2018 (152)
48 EVA_DECODE ss3688977035 Jul 12, 2019 (153)
49 ACPOP ss3728019236 Jul 12, 2019 (153)
50 EVA ss3747554055 Jul 12, 2019 (153)
51 PACBIO ss3783737063 Jul 12, 2019 (153)
52 PACBIO ss3789341925 Jul 12, 2019 (153)
53 PACBIO ss3794214383 Jul 12, 2019 (153)
54 KHV_HUMAN_GENOMES ss3800557561 Jul 12, 2019 (153)
55 1000Genomes NC_000001.10 - 241231375 Oct 11, 2018 (152)
56 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 241231375 Oct 11, 2018 (152)
57 gnomAD - Genomes NC_000001.10 - 241231375 Jul 12, 2019 (153)
58 Northern Sweden NC_000001.10 - 241231375 Jul 12, 2019 (153)
59 TopMed NC_000001.11 - 241068075 Oct 11, 2018 (152)
60 UK 10K study - Twins NC_000001.10 - 241231375 Oct 11, 2018 (152)
61 A Vietnamese Genetic Variation Database NC_000001.10 - 241231375 Jul 12, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77431980, ss78304215 NC_000001.8:237557415:A:G NC_000001.11:241068074:A:G (self)
ss88032372, ss109091792, ss112037513, ss119271450, ss165935373, ss205062064, ss276289263, ss284260760, ss290770889, ss1585735983 NC_000001.9:239297997:A:G NC_000001.11:241068074:A:G (self)
6219596, 3446430, 16973561, 1304101, 3446430, 751656, ss218978458, ss230974871, ss238574525, ss648828078, ss1068743452, ss1295339232, ss1426167641, ss1574799680, ss1602509991, ss1645504024, ss1795999062, ss1919553396, ss1967018147, ss2020304339, ss2148342292, ss2334157284, ss2624665574, ss2698345809, ss2768149236, ss2988737977, ss3343996635, ss3728019236, ss3747554055, ss3783737063, ss3789341925, ss3794214383 NC_000001.10:241231374:A:G NC_000001.11:241068074:A:G (self)
33394636, ss2171504650, ss3023914534, ss3107816399, ss3646926893, ss3688977035, ss3800557561 NC_000001.11:241068074:A:G NC_000001.11:241068074:A:G (self)
ss9856549, ss13017565 NT_004836.14:5974733:A:G NC_000001.11:241068074:A:G (self)
ss14154749, ss20593473 NT_004836.15:5989163:A:G NC_000001.11:241068074:A:G (self)
ss3506912, ss98015828, ss106644363, ss138184995, ss142896541, ss156503251 NT_167186.1:34749153:A:G NC_000001.11:241068074:A:G (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 rs2500239

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