Name: rs66490630
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.

rs66490630

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:39807568 (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=0.079399 (21016/264690, TOPMED)
C=0.077118 (10809/140162, GnomAD)
C=0.073891 (9423/127526, GnomAD_exome) (+ 17 more)
C=0.05843 (1803/30858, ALFA)
C=0.13292 (3756/28258, 14KJPN)
C=0.13395 (2245/16760, 8.3KJPN)
C=0.09115 (982/10774, ExAC)
C=0.1131 (724/6404, 1000G_30x)
C=0.1122 (562/5008, 1000G)
C=0.0652 (292/4480, Estonian)
C=0.0418 (161/3854, ALSPAC)
C=0.0391 (145/3708, TWINSUK)
C=0.1747 (510/2920, KOREAN)
C=0.033 (33/998, GoNL)
C=0.027 (16/600, NorthernSweden)
C=0.032 (7/216, Qatari)
C=0.178 (38/214, Vietnamese)
T=0.481 (50/104, SGDP_PRJ)
C=0.03 (1/40, GENOME_DK)
T=0.39 (7/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: GPR176 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	30858	T=0.94157	C=0.05843	0.888198	0.005055	0.106747	8
European	Sub	24732	T=0.95475	C=0.04525	0.912098	0.002588	0.085315	1
African	Sub	3168	T=0.8469	C=0.1531	0.718434	0.024621	0.256944	0
African Others	Sub	124	T=0.871	C=0.129	0.758065	0.016129	0.225806	0
African American	Sub	3044	T=0.8459	C=0.1541	0.71682	0.024967	0.258213	0
Asian	Sub	128	T=0.859	C=0.141	0.71875	0.0	0.28125	1
East Asian	Sub	100	T=0.87	C=0.13	0.74	0.0	0.26	1
Other Asian	Sub	28	T=0.82	C=0.18	0.642857	0.0	0.357143	0
Latin American 1	Sub	168	T=0.970	C=0.030	0.940476	0.0	0.059524	0
Latin American 2	Sub	700	T=0.931	C=0.069	0.862857	0.0	0.137143	1
South Asian	Sub	114	T=0.833	C=0.167	0.684211	0.017544	0.298246	0
Other	Sub	1848	T=0.9410	C=0.0590	0.888528	0.006494	0.104978	2

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=0.920601	C=0.079399
gnomAD - Genomes	Global	Study-wide	140162	T=0.922882	C=0.077118
gnomAD - Genomes	European	Sub	75930	T=0.95614	C=0.04386
gnomAD - Genomes	African	Sub	41972	T=0.85931	C=0.14069
gnomAD - Genomes	American	Sub	13662	T=0.95096	C=0.04904
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.9642	C=0.0358
gnomAD - Genomes	East Asian	Sub	3128	T=0.8005	C=0.1995
gnomAD - Genomes	Other	Sub	2150	T=0.9251	C=0.0749
gnomAD - Exomes	Global	Study-wide	127526	T=0.926109	C=0.073891
gnomAD - Exomes	European	Sub	52578	T=0.95840	C=0.04160
gnomAD - Exomes	Asian	Sub	32602	T=0.86372	C=0.13628
gnomAD - Exomes	American	Sub	24200	T=0.93926	C=0.06074
gnomAD - Exomes	Ashkenazi Jewish	Sub	8094	T=0.9674	C=0.0326
gnomAD - Exomes	African	Sub	6078	T=0.8567	C=0.1433
gnomAD - Exomes	Other	Sub	3974	T=0.9527	C=0.0473
Allele Frequency Aggregator	Total	Global	30858	T=0.94157	C=0.05843
Allele Frequency Aggregator	European	Sub	24732	T=0.95475	C=0.04525
Allele Frequency Aggregator	African	Sub	3168	T=0.8469	C=0.1531
Allele Frequency Aggregator	Other	Sub	1848	T=0.9410	C=0.0590
Allele Frequency Aggregator	Latin American 2	Sub	700	T=0.931	C=0.069
Allele Frequency Aggregator	Latin American 1	Sub	168	T=0.970	C=0.030
Allele Frequency Aggregator	Asian	Sub	128	T=0.859	C=0.141
Allele Frequency Aggregator	South Asian	Sub	114	T=0.833	C=0.167
14KJPN	JAPANESE	Study-wide	28258	T=0.86708	C=0.13292
8.3KJPN	JAPANESE	Study-wide	16760	T=0.86605	C=0.13395
ExAC	Global	Study-wide	10774	T=0.90885	C=0.09115
ExAC	Asian	Sub	7638	T=0.8905	C=0.1095
ExAC	Europe	Sub	2736	T=0.9653	C=0.0347
ExAC	African	Sub	190	T=0.837	C=0.163
ExAC	Other	Sub	118	T=0.898	C=0.102
ExAC	American	Sub	92	T=0.91	C=0.09
1000Genomes_30x	Global	Study-wide	6404	T=0.8869	C=0.1131
1000Genomes_30x	African	Sub	1786	T=0.8387	C=0.1613
1000Genomes_30x	Europe	Sub	1266	T=0.9684	C=0.0316
1000Genomes_30x	South Asian	Sub	1202	T=0.8785	C=0.1215
1000Genomes_30x	East Asian	Sub	1170	T=0.8265	C=0.1735
1000Genomes_30x	American	Sub	980	T=0.952	C=0.048
1000Genomes	Global	Study-wide	5008	T=0.8878	C=0.1122
1000Genomes	African	Sub	1322	T=0.8427	C=0.1573
1000Genomes	East Asian	Sub	1008	T=0.8254	C=0.1746
1000Genomes	Europe	Sub	1006	T=0.9702	C=0.0298
1000Genomes	South Asian	Sub	978	T=0.884	C=0.116
1000Genomes	American	Sub	694	T=0.950	C=0.050
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9348	C=0.0652
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9582	C=0.0418
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9609	C=0.0391
KOREAN population from KRGDB	KOREAN	Study-wide	2920	T=0.8253	C=0.1747
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.967	C=0.033
Northern Sweden	ACPOP	Study-wide	600	T=0.973	C=0.027
Qatari	Global	Study-wide	216	T=0.968	C=0.032
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.822	C=0.178
SGDP_PRJ	Global	Study-wide	104	T=0.481	C=0.519
The Danish reference pan genome	Danish	Study-wide	40	T=0.97	C=0.03
Siberian	Global	Study-wide	18	T=0.39	C=0.61

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 15	NC_000015.10:g.39807568T>C
GRCh37.p13 chr 15	NC_000015.9:g.40099769T>C

Gene: GPR176, G protein-coupled receptor 176 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GPR176 transcript variant 3	NM_001271855.2:c.38-310A>G	N/A	Intron Variant
GPR176 transcript variant 1	NM_007223.3:c.173-310A>G	N/A	Intron Variant
GPR176 transcript variant 2	NM_001271854.2:c.230A>G	K [AAG] > R [AGG]	Coding Sequence Variant
G-protein coupled receptor 176 isoform 2	NP_001258783.1:p.Lys77Arg	K (Lys) > R (Arg)	Missense Variant
GPR176 transcript variant X1	XM_011521167.4:c.77-310A>G	N/A	Intron Variant
GPR176 transcript variant X2	XM_017021873.3:c.77-310A>G	N/A	Intron Variant
GPR176 transcript variant X5	XM_017021878.3:c.-64-5314… XM_017021878.3:c.-64-5314A>G	N/A	Intron Variant
GPR176 transcript variant X3	XM_017021874.3:c.	N/A	Genic Upstream Transcript Variant
GPR176 transcript variant X4	XM_024449835.2: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=	C
GRCh38.p14 chr 15	NC_000015.10:g.39807568=	NC_000015.10:g.39807568T>C
GRCh37.p13 chr 15	NC_000015.9:g.40099769=	NC_000015.9:g.40099769T>C
GPR176 transcript variant 2	NM_001271854.2:c.230=	NM_001271854.2:c.230A>G
GPR176 transcript variant 2	NM_001271854.1:c.230=	NM_001271854.1:c.230A>G
G-protein coupled receptor 176 isoform 2	NP_001258783.1:p.Lys77=	NP_001258783.1:p.Lys77Arg
GPR176 transcript variant 3	NM_001271855.1:c.38-310=	NM_001271855.1:c.38-310A>G
GPR176 transcript variant 3	NM_001271855.2:c.38-310=	NM_001271855.2:c.38-310A>G
GPR176 transcript variant 1	NM_007223.2:c.173-310=	NM_007223.2:c.173-310A>G
GPR176 transcript variant 1	NM_007223.3:c.173-310=	NM_007223.3:c.173-310A>G
GPR176 transcript variant X1	XM_005254139.1:c.17-310=	XM_005254139.1:c.17-310A>G
GPR176 transcript variant X1	XM_011521167.4:c.77-310=	XM_011521167.4:c.77-310A>G
GPR176 transcript variant X2	XM_017021873.3:c.77-310=	XM_017021873.3:c.77-310A>G
GPR176 transcript variant X5	XM_017021878.3:c.-64-5314=	XM_017021878.3:c.-64-5314A>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#.

70 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss108756944	Feb 13, 2009 (130)
2	1000GENOMES	ss114065131	Feb 03, 2009 (130)
3	COMPLETE_GENOMICS	ss169219480	Jul 04, 2010 (132)
4	BUSHMAN	ss200747860	Jul 04, 2010 (132)
5	1000GENOMES	ss226853776	Jul 14, 2010 (132)
6	1000GENOMES	ss236751924	Jul 15, 2010 (132)
7	1000GENOMES	ss243142936	Jul 15, 2010 (132)
8	GMI	ss282225111	May 04, 2012 (137)
9	ILLUMINA	ss483390443	May 04, 2012 (137)
10	ILLUMINA	ss484154206	May 04, 2012 (137)
11	ILLUMINA	ss536343590	Sep 08, 2015 (146)
12	TISHKOFF	ss564432926	Apr 25, 2013 (138)
13	SSMP	ss660150649	Apr 25, 2013 (138)
14	ILLUMINA	ss780547164	Sep 08, 2015 (146)
15	ILLUMINA	ss782522878	Sep 08, 2015 (146)
16	ILLUMINA	ss836039134	Sep 08, 2015 (146)
17	EVA-GONL	ss991704613	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1080063234	Aug 21, 2014 (142)
19	1000GENOMES	ss1353132135	Aug 21, 2014 (142)
20	DDI	ss1427601314	Apr 01, 2015 (144)
21	EVA_GENOME_DK	ss1577572566	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1632824930	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1675818963	Apr 01, 2015 (144)
24	EVA_EXAC	ss1691749344	Apr 01, 2015 (144)
25	EVA_DECODE	ss1695717995	Apr 01, 2015 (144)
26	WEILL_CORNELL_DGM	ss1935109688	Feb 12, 2016 (147)
27	JJLAB	ss2028334640	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2156731736	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2206100745	Dec 20, 2016 (150)
30	SYSTEMSBIOZJU	ss2628661291	Nov 08, 2017 (151)
31	ILLUMINA	ss2633219278	Nov 08, 2017 (151)
32	GRF	ss2701198200	Nov 08, 2017 (151)
33	GNOMAD	ss2741120628	Nov 08, 2017 (151)
34	GNOMAD	ss2749268190	Nov 08, 2017 (151)
35	GNOMAD	ss2933929945	Nov 08, 2017 (151)
36	SWEGEN	ss3013147733	Nov 08, 2017 (151)
37	CSHL	ss3351080979	Nov 08, 2017 (151)
38	ILLUMINA	ss3627341712	Oct 12, 2018 (152)
39	ILLUMINA	ss3631212972	Oct 12, 2018 (152)
40	ILLUMINA	ss3641909198	Oct 12, 2018 (152)
41	BIOINF_KMB_FNS_UNIBA	ss3645378167	Oct 12, 2018 (152)
42	OMUKHERJEE_ADBS	ss3646472483	Oct 12, 2018 (152)
43	EGCUT_WGS	ss3680293557	Jul 13, 2019 (153)
44	EVA_DECODE	ss3697733684	Jul 13, 2019 (153)
45	ACPOP	ss3740856549	Jul 13, 2019 (153)
46	EVA	ss3752984187	Jul 13, 2019 (153)
47	KHV_HUMAN_GENOMES	ss3818303971	Jul 13, 2019 (153)
48	EVA	ss3834195908	Apr 27, 2020 (154)
49	SGDP_PRJ	ss3882746013	Apr 27, 2020 (154)
50	KRGDB	ss3931879469	Apr 27, 2020 (154)
51	FSA-LAB	ss3984069907	Apr 26, 2021 (155)
52	EVA	ss3986642018	Apr 26, 2021 (155)
53	TOPMED	ss4988401460	Apr 26, 2021 (155)
54	TOMMO_GENOMICS	ss5215797533	Apr 26, 2021 (155)
55	EVA	ss5236922385	Apr 26, 2021 (155)
56	1000G_HIGH_COVERAGE	ss5298150989	Oct 16, 2022 (156)
57	EVA	ss5315778282	Oct 16, 2022 (156)
58	EVA	ss5418703148	Oct 16, 2022 (156)
59	HUGCELL_USP	ss5491912466	Oct 16, 2022 (156)
60	EVA	ss5511403538	Oct 16, 2022 (156)
61	1000G_HIGH_COVERAGE	ss5599406574	Oct 16, 2022 (156)
62	SANFORD_IMAGENETICS	ss5657347187	Oct 16, 2022 (156)
63	TOMMO_GENOMICS	ss5769482113	Oct 16, 2022 (156)
64	YY_MCH	ss5815262344	Oct 16, 2022 (156)
65	EVA	ss5828092781	Oct 16, 2022 (156)
66	EVA	ss5848398258	Oct 16, 2022 (156)
67	EVA	ss5851259941	Oct 16, 2022 (156)
68	EVA	ss5875545062	Oct 16, 2022 (156)
69	EVA	ss5936559882	Oct 16, 2022 (156)
70	EVA	ss5948743819	Oct 16, 2022 (156)
71	1000Genomes	NC_000015.9 - 40099769	Oct 12, 2018 (152)
72	1000Genomes_30x	NC_000015.10 - 39807568	Oct 16, 2022 (156)
73	The Avon Longitudinal Study of Parents and Children	NC_000015.9 - 40099769	Oct 12, 2018 (152)
74	Genetic variation in the Estonian population	NC_000015.9 - 40099769	Oct 12, 2018 (152)
75	ExAC	NC_000015.9 - 40099769	Oct 12, 2018 (152)
76	The Danish reference pan genome	NC_000015.9 - 40099769	Apr 27, 2020 (154)
77	gnomAD - Genomes	NC_000015.10 - 39807568	Apr 26, 2021 (155)
78	gnomAD - Exomes	NC_000015.9 - 40099769	Jul 13, 2019 (153)
79	Genome of the Netherlands Release 5	NC_000015.9 - 40099769	Apr 27, 2020 (154)
80	KOREAN population from KRGDB	NC_000015.9 - 40099769	Apr 27, 2020 (154)
81	Northern Sweden	NC_000015.9 - 40099769	Jul 13, 2019 (153)
82	Qatari	NC_000015.9 - 40099769	Apr 27, 2020 (154)
83	SGDP_PRJ	NC_000015.9 - 40099769	Apr 27, 2020 (154)
84	Siberian	NC_000015.9 - 40099769	Apr 27, 2020 (154)
85	8.3KJPN	NC_000015.9 - 40099769	Apr 26, 2021 (155)
86	14KJPN	NC_000015.10 - 39807568	Oct 16, 2022 (156)
87	TopMed	NC_000015.10 - 39807568	Apr 26, 2021 (155)
88	UK 10K study - Twins	NC_000015.9 - 40099769	Oct 12, 2018 (152)
89	A Vietnamese Genetic Variation Database	NC_000015.9 - 40099769	Jul 13, 2019 (153)
90	ALFA	NC_000015.10 - 39807568	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
ss108756944, ss114065131, ss169219480, ss200747860, ss282225111, ss483390443, ss1695717995	NC_000015.8:37887060:T:C	NC_000015.10:39807567:T:C	(self)
66191760, 36746012, 26031805, 2116604, 3826171, 10382467, 16415696, 39056863, 14141414, 17151618, 34762993, 9248090, 73766840, 36746012, 8176393, ss226853776, ss236751924, ss243142936, ss484154206, ss536343590, ss564432926, ss660150649, ss780547164, ss782522878, ss836039134, ss991704613, ss1080063234, ss1353132135, ss1427601314, ss1577572566, ss1632824930, ss1675818963, ss1691749344, ss1935109688, ss2028334640, ss2156731736, ss2628661291, ss2633219278, ss2701198200, ss2741120628, ss2749268190, ss2933929945, ss3013147733, ss3351080979, ss3627341712, ss3631212972, ss3641909198, ss3646472483, ss3680293557, ss3740856549, ss3752984187, ss3834195908, ss3882746013, ss3931879469, ss3984069907, ss3986642018, ss5215797533, ss5315778282, ss5418703148, ss5511403538, ss5657347187, ss5828092781, ss5848398258, ss5936559882, ss5948743819	NC_000015.9:40099768:T:C	NC_000015.10:39807567:T:C	(self)
86932509, 466581941, 103319217, 203947120, 3530735617, ss2206100745, ss3645378167, ss3697733684, ss3818303971, ss4988401460, ss5236922385, ss5298150989, ss5491912466, ss5599406574, ss5769482113, ss5815262344, ss5851259941, ss5875545062	NC_000015.10:39807567:T:C	NC_000015.10:39807567: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 rs66490630

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs66490630