Name: rs112007886
Published: September 21, 2022
License: Open Access

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.

rs112007886

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:65182776 (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: T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.044138 (11683/264690, TOPMED)
C=0.044516 (6241/140196, GnomAD)
C=0.03277 (619/18890, ALFA) (+ 12 more)
C=0.0381 (244/6404, 1000G_30x)
C=0.0381 (191/5008, 1000G)
C=0.0156 (70/4480, Estonian)
C=0.0265 (102/3854, ALSPAC)
C=0.0224 (83/3708, TWINSUK)
C=0.0003 (1/2920, KOREAN)
C=0.028 (28/998, GoNL)
C=0.008 (5/600, NorthernSweden)
C=0.051 (11/216, Qatari)
C=0.05 (2/40, GENOME_DK)
T=0.50 (11/22, SGDP_PRJ)
C=0.50 (11/22, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RGS9 : Intron 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	18890	T=0.96723	C=0.03277
European	Sub	14286	T=0.97606	C=0.02394
African	Sub	2946	T=0.9267	C=0.0733
African Others	Sub	114	T=0.895	C=0.105
African American	Sub	2832	T=0.9280	C=0.0720
Asian	Sub	112	T=1.000	C=0.000
East Asian	Sub	86	T=1.00	C=0.00
Other Asian	Sub	26	T=1.00	C=0.00
Latin American 1	Sub	146	T=0.932	C=0.068
Latin American 2	Sub	610	T=0.972	C=0.028
South Asian	Sub	98	T=0.99	C=0.01
Other	Sub	692	T=0.952	C=0.048

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	264690	T=0.955862	C=0.044138
gnomAD - Genomes	Global	Study-wide	140196	T=0.955484	C=0.044516
gnomAD - Genomes	European	Sub	75930	T=0.97112	C=0.02888
gnomAD - Genomes	African	Sub	42014	T=0.91965	C=0.08035
gnomAD - Genomes	American	Sub	13644	T=0.96790	C=0.03210
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.9582	C=0.0418
gnomAD - Genomes	East Asian	Sub	3132	T=0.9997	C=0.0003
gnomAD - Genomes	Other	Sub	2154	T=0.9564	C=0.0436
Allele Frequency Aggregator	Total	Global	18890	T=0.96723	C=0.03277
Allele Frequency Aggregator	European	Sub	14286	T=0.97606	C=0.02394
Allele Frequency Aggregator	African	Sub	2946	T=0.9267	C=0.0733
Allele Frequency Aggregator	Other	Sub	692	T=0.952	C=0.048
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.972	C=0.028
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.932	C=0.068
Allele Frequency Aggregator	Asian	Sub	112	T=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=0.99	C=0.01
1000Genomes_30x	Global	Study-wide	6404	T=0.9619	C=0.0381
1000Genomes_30x	African	Sub	1786	T=0.9031	C=0.0969
1000Genomes_30x	Europe	Sub	1266	T=0.9652	C=0.0348
1000Genomes_30x	South Asian	Sub	1202	T=0.9967	C=0.0033
1000Genomes_30x	East Asian	Sub	1170	T=0.9991	C=0.0009
1000Genomes_30x	American	Sub	980	T=0.978	C=0.022
1000Genomes	Global	Study-wide	5008	T=0.9619	C=0.0381
1000Genomes	African	Sub	1322	T=0.8979	C=0.1021
1000Genomes	East Asian	Sub	1008	T=0.9990	C=0.0010
1000Genomes	Europe	Sub	1006	T=0.9672	C=0.0328
1000Genomes	South Asian	Sub	978	T=0.996	C=0.004
1000Genomes	American	Sub	694	T=0.974	C=0.026
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9844	C=0.0156
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9735	C=0.0265
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9776	C=0.0224
KOREAN population from KRGDB	KOREAN	Study-wide	2920	T=0.9997	C=0.0003
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.972	C=0.028
Northern Sweden	ACPOP	Study-wide	600	T=0.992	C=0.008
Qatari	Global	Study-wide	216	T=0.949	C=0.051
The Danish reference pan genome	Danish	Study-wide	40	T=0.95	C=0.05
SGDP_PRJ	Global	Study-wide	22	T=0.50	C=0.50

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 17	NC_000017.11:g.65182776T>C
GRCh37.p13 chr 17	NC_000017.10:g.63178894T>C
RGS9 RefSeqGene	NG_013021.2:g.50439T>C

Gene: RGS9, regulator of G protein signaling 9 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RGS9 transcript variant 2	NM_001081955.3:c.645+4982… NM_001081955.3:c.645+4982T>C	N/A	Intron Variant
RGS9 transcript variant 3	NM_001165933.2:c.645+4982… NM_001165933.2:c.645+4982T>C	N/A	Intron Variant
RGS9 transcript variant 1	NM_003835.4:c.654+4973T>C	N/A	Intron Variant

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

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
GRCh38.p14 chr 17	NC_000017.11:g.65182776=	NC_000017.11:g.65182776T>C
GRCh37.p13 chr 17	NC_000017.10:g.63178894=	NC_000017.10:g.63178894T>C
RGS9 RefSeqGene	NG_013021.2:g.50439=	NG_013021.2:g.50439T>C
RGS9 transcript variant 2	NM_001081955.2:c.645+4982=	NM_001081955.2:c.645+4982T>C
RGS9 transcript variant 2	NM_001081955.3:c.645+4982=	NM_001081955.3:c.645+4982T>C
RGS9 transcript variant 3	NM_001165933.1:c.645+4982=	NM_001165933.1:c.645+4982T>C
RGS9 transcript variant 3	NM_001165933.2:c.645+4982=	NM_001165933.2:c.645+4982T>C
RGS9 transcript variant 1	NM_003835.3:c.654+4973=	NM_003835.3:c.654+4973T>C
RGS9 transcript variant 1	NM_003835.4:c.654+4973=	NM_003835.4:c.654+4973T>C

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#.

34 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BUSHMAN	ss202689855	Jul 04, 2010 (132)
2	1000GENOMES	ss339797401	May 09, 2011 (134)
3	TISHKOFF	ss565358999	Apr 25, 2013 (138)
4	EVA-GONL	ss993257100	Aug 21, 2014 (142)
5	JMKIDD_LAB	ss1081159631	Aug 21, 2014 (142)
6	1000GENOMES	ss1359249724	Aug 21, 2014 (142)
7	DDI	ss1428074650	Apr 01, 2015 (144)
8	EVA_GENOME_DK	ss1578213094	Apr 01, 2015 (144)
9	EVA_UK10K_ALSPAC	ss1635950918	Apr 01, 2015 (144)
10	EVA_UK10K_TWINSUK	ss1678944951	Apr 01, 2015 (144)
11	EVA_DECODE	ss1697304756	Apr 01, 2015 (144)
12	WEILL_CORNELL_DGM	ss1936717816	Feb 12, 2016 (147)
13	JJLAB	ss2029130785	Sep 14, 2016 (149)
14	HUMAN_LONGEVITY	ss2218031829	Dec 20, 2016 (150)
15	GNOMAD	ss2951638588	Nov 08, 2017 (151)
16	SWEGEN	ss3015782061	Nov 08, 2017 (151)
17	CSHL	ss3351804808	Nov 08, 2017 (151)
18	EGCUT_WGS	ss3682649583	Jul 13, 2019 (153)
19	EVA_DECODE	ss3700765104	Jul 13, 2019 (153)
20	ACPOP	ss3742150069	Jul 13, 2019 (153)
21	EVA	ss3754841196	Jul 13, 2019 (153)
22	KHV_HUMAN_GENOMES	ss3820107232	Jul 13, 2019 (153)
23	SGDP_PRJ	ss3886059958	Apr 27, 2020 (154)
24	KRGDB	ss3935811084	Apr 27, 2020 (154)
25	TOPMED	ss5041346394	Apr 26, 2021 (155)
26	1000G_HIGH_COVERAGE	ss5303670837	Oct 16, 2022 (156)
27	EVA	ss5428554811	Oct 16, 2022 (156)
28	HUGCELL_USP	ss5496657909	Oct 16, 2022 (156)
29	EVA	ss5511807331	Oct 16, 2022 (156)
30	1000G_HIGH_COVERAGE	ss5607653803	Oct 16, 2022 (156)
31	SANFORD_IMAGENETICS	ss5660396508	Oct 16, 2022 (156)
32	EVA	ss5834184882	Oct 16, 2022 (156)
33	EVA	ss5914530080	Oct 16, 2022 (156)
34	EVA	ss5951790759	Oct 16, 2022 (156)
35	1000Genomes	NC_000017.10 - 63178894	Oct 12, 2018 (152)
36	1000Genomes_30x	NC_000017.11 - 65182776	Oct 16, 2022 (156)
37	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 63178894	Oct 12, 2018 (152)
38	Genetic variation in the Estonian population	NC_000017.10 - 63178894	Oct 12, 2018 (152)
39	The Danish reference pan genome	NC_000017.10 - 63178894	Apr 27, 2020 (154)
40	gnomAD - Genomes	NC_000017.11 - 65182776	Apr 26, 2021 (155)
41	Genome of the Netherlands Release 5	NC_000017.10 - 63178894	Apr 27, 2020 (154)
42	KOREAN population from KRGDB	NC_000017.10 - 63178894	Apr 27, 2020 (154)
43	Northern Sweden	NC_000017.10 - 63178894	Jul 13, 2019 (153)
44	Qatari	NC_000017.10 - 63178894	Apr 27, 2020 (154)
45	SGDP_PRJ	NC_000017.10 - 63178894	Apr 27, 2020 (154)
46	TopMed	NC_000017.11 - 65182776	Apr 26, 2021 (155)
47	UK 10K study - Twins	NC_000017.10 - 63178894	Oct 12, 2018 (152)
48	ALFA	NC_000017.11 - 65182776	Apr 26, 2021 (155)

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
ss202689855, ss1697304756	NC_000017.9:60609355:T:C	NC_000017.11:65182775:T:C	(self)
72514533, 40180139, 28387831, 4413177, 17902488, 42988478, 15434934, 18759738, 38076938, 40180139, ss339797401, ss565358999, ss993257100, ss1081159631, ss1359249724, ss1428074650, ss1578213094, ss1635950918, ss1678944951, ss1936717816, ss2029130785, ss2951638588, ss3015782061, ss3351804808, ss3682649583, ss3742150069, ss3754841196, ss3886059958, ss3935811084, ss5428554811, ss5511807331, ss5660396508, ss5834184882, ss5951790759	NC_000017.10:63178893:T:C	NC_000017.11:65182775:T:C	(self)
95179738, 511766891, 256892056, 9709549709, ss2218031829, ss3700765104, ss3820107232, ss5041346394, ss5303670837, ss5496657909, ss5607653803, ss5914530080	NC_000017.11:65182775:T:C	NC_000017.11:65182775:T:C	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs112007886

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs112007886