Name: rs10158313
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.

rs10158313

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:241126480 (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>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.00044 (8/18008, ALFA)
A=0.0545 (349/6404, 1000G_30x)
A=0.0519 (260/5008, 1000G) (+ 8 more)
A=0.0002 (1/4480, Estonian)
A=0.0010 (4/3854, ALSPAC)
A=0.0005 (2/3708, TWINSUK)
A=0.002 (2/998, GoNL)
A=0.028 (6/216, Qatari)
A=0.000 (0/200, HapMap)
T=0.50 (10/20, SGDP_PRJ)
A=0.50 (10/20, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RGS7 : 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	18008	T=0.99956	A=0.00044, C=0.00000
European	Sub	14256	T=0.99993	A=0.00007, C=0.00000
African	Sub	2152	T=0.9991	A=0.0009, C=0.0000
African Others	Sub	86	T=1.00	A=0.00, C=0.00
African American	Sub	2066	T=0.9990	A=0.0010, C=0.0000
Asian	Sub	112	T=1.000	A=0.000, C=0.000
East Asian	Sub	86	T=1.00	A=0.00, C=0.00
Other Asian	Sub	26	T=1.00	A=0.00, C=0.00
Latin American 1	Sub	138	T=1.000	A=0.000, C=0.000
Latin American 2	Sub	606	T=1.000	A=0.000, C=0.000
South Asian	Sub	98	T=1.00	A=0.00, C=0.00
Other	Sub	646	T=0.992	A=0.008, C=0.000

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
Allele Frequency Aggregator	Total	Global	18008	T=0.99956	A=0.00044, C=0.00000
Allele Frequency Aggregator	European	Sub	14256	T=0.99993	A=0.00007, C=0.00000
Allele Frequency Aggregator	African	Sub	2152	T=0.9991	A=0.0009, C=0.0000
Allele Frequency Aggregator	Other	Sub	646	T=0.992	A=0.008, C=0.000
Allele Frequency Aggregator	Latin American 2	Sub	606	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	138	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Asian	Sub	112	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=1.00	A=0.00, C=0.00
1000Genomes_30x	Global	Study-wide	6404	T=0.9455	A=0.0545
1000Genomes_30x	African	Sub	1786	T=0.8108	A=0.1892
1000Genomes_30x	Europe	Sub	1266	T=0.9984	A=0.0016
1000Genomes_30x	South Asian	Sub	1202	T=1.0000	A=0.0000
1000Genomes_30x	East Asian	Sub	1170	T=1.0000	A=0.0000
1000Genomes_30x	American	Sub	980	T=0.991	A=0.009
1000Genomes	Global	Study-wide	5008	T=0.9481	A=0.0519
1000Genomes	African	Sub	1322	T=0.8086	A=0.1914
1000Genomes	East Asian	Sub	1008	T=1.0000	A=0.0000
1000Genomes	Europe	Sub	1006	T=0.9990	A=0.0010
1000Genomes	South Asian	Sub	978	T=1.000	A=0.000
1000Genomes	American	Sub	694	T=0.991	A=0.009
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9998	A=0.0002
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9990	A=0.0010
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9995	A=0.0005
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.998	A=0.002
Qatari	Global	Study-wide	216	T=0.972	A=0.028
HapMap	Global	Study-wide	200	T=1.000	A=0.000
HapMap	American	Sub	114	T=1.000	A=0.000
HapMap	Asian	Sub	86	T=1.00	A=0.00
SGDP_PRJ	Global	Study-wide	20	T=0.50	A=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 1	NC_000001.11:g.241126480T>A
GRCh38.p14 chr 1	NC_000001.11:g.241126480T>C
GRCh37.p13 chr 1	NC_000001.10:g.241289780T>A
GRCh37.p13 chr 1	NC_000001.10:g.241289780T>C

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.79-27718… NM_001282773.2:c.79-27718A>T	N/A	Intron Variant
RGS7 transcript variant 3	NM_001282775.2:c.79-27718… NM_001282775.2:c.79-27718A>T	N/A	Intron Variant
RGS7 transcript variant 4	NM_001282778.2:c.79-27718… NM_001282778.2:c.79-27718A>T	N/A	Intron Variant
RGS7 transcript variant 5	NM_001350113.2:c.1-27718A… NM_001350113.2:c.1-27718A>T	N/A	Intron Variant
RGS7 transcript variant 6	NM_001350114.2:c.1-27718A… NM_001350114.2:c.1-27718A>T	N/A	Intron Variant
RGS7 transcript variant 7	NM_001350115.2:c.1-27718A… NM_001350115.2:c.1-27718A>T	N/A	Intron Variant
RGS7 transcript variant 8	NM_001350116.1:c.1-27718A… NM_001350116.1:c.1-27718A>T	N/A	Intron Variant
RGS7 transcript variant 9	NM_001364886.1:c.79-27718… NM_001364886.1:c.79-27718A>T	N/A	Intron Variant
RGS7 transcript variant 10	NM_001374806.1:c.79-27718… NM_001374806.1:c.79-27718A>T	N/A	Intron Variant
RGS7 transcript variant 11	NM_001374807.1:c.79-27718… NM_001374807.1:c.79-27718A>T	N/A	Intron Variant
RGS7 transcript variant 12	NM_001374808.1:c.-146-245… NM_001374808.1:c.-146-24502A>T	N/A	Intron Variant
RGS7 transcript variant 13	NM_001374809.1:c.-211-277… NM_001374809.1:c.-211-27718A>T	N/A	Intron Variant
RGS7 transcript variant 14	NM_001374810.1:c.-211-277… NM_001374810.1:c.-211-27718A>T	N/A	Intron Variant
RGS7 transcript variant 16	NM_001374811.1:c.79-27718… NM_001374811.1:c.79-27718A>T	N/A	Intron Variant
RGS7 transcript variant 15	NM_001374812.1:c.79-27718… NM_001374812.1:c.79-27718A>T	N/A	Intron Variant
RGS7 transcript variant 17	NM_001374813.1:c.-211-277… NM_001374813.1:c.-211-27718A>T	N/A	Intron Variant
RGS7 transcript variant 18	NM_001374814.1:c.79-27718… NM_001374814.1:c.79-27718A>T	N/A	Intron Variant
RGS7 transcript variant 19	NM_001374815.1:c.79-27718… NM_001374815.1:c.79-27718A>T	N/A	Intron Variant
RGS7 transcript variant 20	NM_001374816.1:c.79-27718… NM_001374816.1:c.79-27718A>T	N/A	Intron Variant
RGS7 transcript variant 1	NM_002924.6:c.79-27718A>T	N/A	Intron Variant
RGS7 transcript variant X1	XM_047426980.1:c.-1+8387A… XM_047426980.1:c.-1+8387A>T	N/A	Intron Variant
RGS7 transcript variant X2	XM_017002009.2:c.	N/A	Genic Upstream Transcript 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=	A	C
GRCh38.p14 chr 1	NC_000001.11:g.241126480=	NC_000001.11:g.241126480T>A	NC_000001.11:g.241126480T>C
GRCh37.p13 chr 1	NC_000001.10:g.241289780=	NC_000001.10:g.241289780T>A	NC_000001.10:g.241289780T>C
RGS7 transcript variant 2	NM_001282773.2:c.79-27718=	NM_001282773.2:c.79-27718A>T	NM_001282773.2:c.79-27718A>G
RGS7 transcript variant 3	NM_001282775.2:c.79-27718=	NM_001282775.2:c.79-27718A>T	NM_001282775.2:c.79-27718A>G
RGS7 transcript variant 4	NM_001282778.2:c.79-27718=	NM_001282778.2:c.79-27718A>T	NM_001282778.2:c.79-27718A>G
RGS7 transcript variant 5	NM_001350113.2:c.1-27718=	NM_001350113.2:c.1-27718A>T	NM_001350113.2:c.1-27718A>G
RGS7 transcript variant 6	NM_001350114.2:c.1-27718=	NM_001350114.2:c.1-27718A>T	NM_001350114.2:c.1-27718A>G
RGS7 transcript variant 7	NM_001350115.2:c.1-27718=	NM_001350115.2:c.1-27718A>T	NM_001350115.2:c.1-27718A>G
RGS7 transcript variant 8	NM_001350116.1:c.1-27718=	NM_001350116.1:c.1-27718A>T	NM_001350116.1:c.1-27718A>G
RGS7 transcript variant 9	NM_001364886.1:c.79-27718=	NM_001364886.1:c.79-27718A>T	NM_001364886.1:c.79-27718A>G
RGS7 transcript variant 10	NM_001374806.1:c.79-27718=	NM_001374806.1:c.79-27718A>T	NM_001374806.1:c.79-27718A>G
RGS7 transcript variant 11	NM_001374807.1:c.79-27718=	NM_001374807.1:c.79-27718A>T	NM_001374807.1:c.79-27718A>G
RGS7 transcript variant 12	NM_001374808.1:c.-146-24502=	NM_001374808.1:c.-146-24502A>T	NM_001374808.1:c.-146-24502A>G
RGS7 transcript variant 13	NM_001374809.1:c.-211-27718=	NM_001374809.1:c.-211-27718A>T	NM_001374809.1:c.-211-27718A>G
RGS7 transcript variant 14	NM_001374810.1:c.-211-27718=	NM_001374810.1:c.-211-27718A>T	NM_001374810.1:c.-211-27718A>G
RGS7 transcript variant 16	NM_001374811.1:c.79-27718=	NM_001374811.1:c.79-27718A>T	NM_001374811.1:c.79-27718A>G
RGS7 transcript variant 15	NM_001374812.1:c.79-27718=	NM_001374812.1:c.79-27718A>T	NM_001374812.1:c.79-27718A>G
RGS7 transcript variant 17	NM_001374813.1:c.-211-27718=	NM_001374813.1:c.-211-27718A>T	NM_001374813.1:c.-211-27718A>G
RGS7 transcript variant 18	NM_001374814.1:c.79-27718=	NM_001374814.1:c.79-27718A>T	NM_001374814.1:c.79-27718A>G
RGS7 transcript variant 19	NM_001374815.1:c.79-27718=	NM_001374815.1:c.79-27718A>T	NM_001374815.1:c.79-27718A>G
RGS7 transcript variant 20	NM_001374816.1:c.79-27718=	NM_001374816.1:c.79-27718A>T	NM_001374816.1:c.79-27718A>G
RGS7 transcript	NM_002924.4:c.79-27718=	NM_002924.4:c.79-27718A>T	NM_002924.4:c.79-27718A>G
RGS7 transcript variant 1	NM_002924.6:c.79-27718=	NM_002924.6:c.79-27718A>T	NM_002924.6:c.79-27718A>G
RGS7 transcript variant X1	XM_005273218.1:c.79-27718=	XM_005273218.1:c.79-27718A>T	XM_005273218.1:c.79-27718A>G
RGS7 transcript variant X2	XM_005273219.1:c.79-27718=	XM_005273219.1:c.79-27718A>T	XM_005273219.1:c.79-27718A>G
RGS7 transcript variant X3	XM_005273220.1:c.79-27718=	XM_005273220.1:c.79-27718A>T	XM_005273220.1:c.79-27718A>G
RGS7 transcript variant X4	XM_005273221.1:c.1-27718=	XM_005273221.1:c.1-27718A>T	XM_005273221.1:c.1-27718A>G
RGS7 transcript variant X5	XM_005273222.1:c.79-27718=	XM_005273222.1:c.79-27718A>T	XM_005273222.1:c.79-27718A>G
RGS7 transcript variant X6	XM_005273223.1:c.79-27718=	XM_005273223.1:c.79-27718A>T	XM_005273223.1:c.79-27718A>G
RGS7 transcript variant X1	XM_047426980.1:c.-1+8387=	XM_047426980.1:c.-1+8387A>T	XM_047426980.1:c.-1+8387A>G

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#.

30 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WUGSC_SSAHASNP	ss14019320	Dec 05, 2003 (119)
2	1000GENOMES	ss112038502	Jan 25, 2009 (130)
3	COMPLETE_GENOMICS	ss165540601	Jul 04, 2010 (132)
4	BUSHMAN	ss199839186	Jul 04, 2010 (132)
5	1000GENOMES	ss218978759	Jul 14, 2010 (132)
6	1000GENOMES	ss230975073	Jul 14, 2010 (132)
7	TISHKOFF	ss555254309	Apr 25, 2013 (138)
8	EVA-GONL	ss976332230	Aug 21, 2014 (142)
9	1000GENOMES	ss1295340936	Aug 21, 2014 (142)
10	EVA_UK10K_ALSPAC	ss1602510931	Apr 01, 2015 (144)
11	EVA_UK10K_TWINSUK	ss1645504964	Apr 01, 2015 (144)
12	HAMMER_LAB	ss1795999897	Sep 08, 2015 (146)
13	WEILL_CORNELL_DGM	ss1919553954	Feb 12, 2016 (147)
14	HUMAN_LONGEVITY	ss2171508264	Dec 20, 2016 (150)
15	GNOMAD	ss2768153960	Nov 08, 2017 (151)
16	EGCUT_WGS	ss3656699926	Jul 12, 2019 (153)
17	EVA_DECODE	ss3688978013	Jul 12, 2019 (153)
18	KHV_HUMAN_GENOMES	ss3800558168	Jul 12, 2019 (153)
19	SGDP_PRJ	ss3851264085	Apr 25, 2020 (154)
20	TOPMED	ss4489528424	Apr 27, 2021 (155)
21	TOPMED	ss4489528425	Apr 27, 2021 (155)
22	1000G_HIGH_COVERAGE	ss5246403006	Oct 12, 2022 (156)
23	EVA	ss5325893404	Oct 12, 2022 (156)
24	HUGCELL_USP	ss5446782422	Oct 12, 2022 (156)
25	EVA	ss5506249805	Oct 12, 2022 (156)
26	1000G_HIGH_COVERAGE	ss5520802002	Oct 12, 2022 (156)
27	SANFORD_IMAGENETICS	ss5627795527	Oct 12, 2022 (156)
28	EVA	ss5833510455	Oct 12, 2022 (156)
29	EVA	ss5912670987	Oct 12, 2022 (156)
30	EVA	ss5939646077	Oct 12, 2022 (156)
31	1000Genomes	NC_000001.10 - 241289780	Oct 11, 2018 (152)
32	1000Genomes_30x	NC_000001.11 - 241126480	Oct 12, 2022 (156)
33	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 241289780	Oct 11, 2018 (152)
34	Genetic variation in the Estonian population	NC_000001.10 - 241289780	Oct 11, 2018 (152)
35	gnomAD - Genomes Submission ignored due to conflicting rows: Row 44511781 (NC_000001.11:241126479:T:A 6019/140188) Row 44511782 (NC_000001.11:241126479:T:C 2/140208)	-	Apr 27, 2021 (155)
36	gnomAD - Genomes Submission ignored due to conflicting rows: Row 44511781 (NC_000001.11:241126479:T:A 6019/140188) Row 44511782 (NC_000001.11:241126479:T:C 2/140208)	-	Apr 27, 2021 (155)
37	Genome of the Netherlands Release 5	NC_000001.10 - 241289780	Apr 25, 2020 (154)
38	HapMap	NC_000001.11 - 241126480	Apr 25, 2020 (154)
39	Qatari	NC_000001.10 - 241289780	Apr 25, 2020 (154)
40	SGDP_PRJ	NC_000001.10 - 241289780	Apr 25, 2020 (154)
41	TopMed Submission ignored due to conflicting rows: Row 53134759 (NC_000001.11:241126479:T:A 12041/264690) Row 53134760 (NC_000001.11:241126479:T:C 3/264690)	-	Apr 27, 2021 (155)
42	TopMed Submission ignored due to conflicting rows: Row 53134759 (NC_000001.11:241126479:T:A 12041/264690) Row 53134760 (NC_000001.11:241126479:T:C 3/264690)	-	Apr 27, 2021 (155)
43	UK 10K study - Twins	NC_000001.10 - 241289780	Oct 11, 2018 (152)
44	ALFA	NC_000001.11 - 241126480	Apr 27, 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
ss112038502, ss165540601, ss199839186	NC_000001.9:239356402:T:A	NC_000001.11:241126479:T:A	(self)
6221388, 3447478, 2438174, 1510274, 1595884, 3281065, 3447478, ss218978759, ss230975073, ss555254309, ss976332230, ss1295340936, ss1602510931, ss1645504964, ss1795999897, ss1919553954, ss2768153960, ss3656699926, ss3851264085, ss5325893404, ss5506249805, ss5627795527, ss5833510455, ss5939646077	NC_000001.10:241289779:T:A	NC_000001.11:241126479:T:A	(self)
8327937, 306305, 12642807429, ss2171508264, ss3688978013, ss3800558168, ss4489528424, ss5246403006, ss5446782422, ss5520802002, ss5912670987	NC_000001.11:241126479:T:A	NC_000001.11:241126479:T:A	(self)
ss14019320	NT_004836.15:6047568:T:A	NC_000001.11:241126479:T:A	(self)
12642807429, ss4489528425	NC_000001.11:241126479:T:C	NC_000001.11:241126479: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 rs10158313

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

rs10158313