Name: rs1391875
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.

rs1391875

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:88714478 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.216899 (57411/264690, TOPMED)
C=0.219291 (30663/139828, GnomAD)
C=0.19336 (5464/28258, 14KJPN) (+ 17 more)
C=0.23277 (4397/18890, ALFA)
C=0.19322 (3238/16758, 8.3KJPN)
C=0.1688 (1081/6404, 1000G_30x)
C=0.1669 (836/5008, 1000G)
C=0.2165 (970/4480, Estonian)
C=0.2800 (1079/3854, ALSPAC)
C=0.2602 (965/3708, TWINSUK)
C=0.1655 (485/2930, KOREAN)
C=0.2007 (377/1878, HapMap)
C=0.1829 (335/1832, Korea1K)
C=0.243 (243/998, GoNL)
C=0.228 (137/600, NorthernSweden)
C=0.185 (40/216, Qatari)
C=0.106 (23/216, Vietnamese)
G=0.422 (76/180, SGDP_PRJ)
C=0.17 (7/40, GENOME_DK)
G=0.35 (12/34, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: GRM5 : 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	G=0.76723	C=0.23277
European	Sub	14286	G=0.74920	C=0.25080
African	Sub	2946	G=0.8350	C=0.1650
African Others	Sub	114	G=0.842	C=0.158
African American	Sub	2832	G=0.8347	C=0.1653
Asian	Sub	112	G=0.875	C=0.125
East Asian	Sub	86	G=0.86	C=0.14
Other Asian	Sub	26	G=0.92	C=0.08
Latin American 1	Sub	146	G=0.753	C=0.247
Latin American 2	Sub	610	G=0.815	C=0.185
South Asian	Sub	98	G=0.84	C=0.16
Other	Sub	692	G=0.785	C=0.215

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	G=0.783101	C=0.216899
gnomAD - Genomes	Global	Study-wide	139828	G=0.780709	C=0.219291
gnomAD - Genomes	European	Sub	75762	G=0.74687	C=0.25313
gnomAD - Genomes	African	Sub	41920	G=0.83373	C=0.16627
gnomAD - Genomes	American	Sub	13578	G=0.81124	C=0.18876
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	G=0.6831	C=0.3169
gnomAD - Genomes	East Asian	Sub	3098	G=0.8699	C=0.1301
gnomAD - Genomes	Other	Sub	2150	G=0.7688	C=0.2312
14KJPN	JAPANESE	Study-wide	28258	G=0.80664	C=0.19336
Allele Frequency Aggregator	Total	Global	18890	G=0.76723	C=0.23277
Allele Frequency Aggregator	European	Sub	14286	G=0.74920	C=0.25080
Allele Frequency Aggregator	African	Sub	2946	G=0.8350	C=0.1650
Allele Frequency Aggregator	Other	Sub	692	G=0.785	C=0.215
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.815	C=0.185
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.753	C=0.247
Allele Frequency Aggregator	Asian	Sub	112	G=0.875	C=0.125
Allele Frequency Aggregator	South Asian	Sub	98	G=0.84	C=0.16
8.3KJPN	JAPANESE	Study-wide	16758	G=0.80678	C=0.19322
1000Genomes_30x	Global	Study-wide	6404	G=0.8312	C=0.1688
1000Genomes_30x	African	Sub	1786	G=0.8343	C=0.1657
1000Genomes_30x	Europe	Sub	1266	G=0.7291	C=0.2709
1000Genomes_30x	South Asian	Sub	1202	G=0.9151	C=0.0849
1000Genomes_30x	East Asian	Sub	1170	G=0.8795	C=0.1205
1000Genomes_30x	American	Sub	980	G=0.797	C=0.203
1000Genomes	Global	Study-wide	5008	G=0.8331	C=0.1669
1000Genomes	African	Sub	1322	G=0.8359	C=0.1641
1000Genomes	East Asian	Sub	1008	G=0.8740	C=0.1260
1000Genomes	Europe	Sub	1006	G=0.7376	C=0.2624
1000Genomes	South Asian	Sub	978	G=0.915	C=0.085
1000Genomes	American	Sub	694	G=0.791	C=0.209
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7835	C=0.2165
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.7200	C=0.2800
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7398	C=0.2602
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.8345	C=0.1655
HapMap	Global	Study-wide	1878	G=0.7993	C=0.2007
HapMap	American	Sub	758	G=0.825	C=0.175
HapMap	African	Sub	690	G=0.778	C=0.222
HapMap	Asian	Sub	254	G=0.843	C=0.157
HapMap	Europe	Sub	176	G=0.710	C=0.290
Korean Genome Project	KOREAN	Study-wide	1832	G=0.8171	C=0.1829
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.757	C=0.243
Northern Sweden	ACPOP	Study-wide	600	G=0.772	C=0.228
Qatari	Global	Study-wide	216	G=0.815	C=0.185
A Vietnamese Genetic Variation Database	Global	Study-wide	216	G=0.894	C=0.106
SGDP_PRJ	Global	Study-wide	180	G=0.422	C=0.578
The Danish reference pan genome	Danish	Study-wide	40	G=0.82	C=0.17
Siberian	Global	Study-wide	34	G=0.35	C=0.65

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 11	NC_000011.10:g.88714478G>C
GRCh37.p13 chr 11	NC_000011.9:g.88447646G>C
GRM5 RefSeqGene	NG_052831.1:g.356494C>G

Gene: GRM5, glutamate metabotropic receptor 5 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GRM5 transcript variant b	NM_000842.5:c.912-61075C>G	N/A	Intron Variant
GRM5 transcript variant a	NM_001143831.3:c.912-6107… NM_001143831.3:c.912-61075C>G	N/A	Intron Variant
GRM5 transcript variant c	NM_001384268.1:c.912-6107… NM_001384268.1:c.912-61075C>G	N/A	Intron Variant
GRM5 transcript variant X1	XM_011542792.2:c.912-6107… XM_011542792.2:c.912-61075C>G	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	G=	C
GRCh38.p14 chr 11	NC_000011.10:g.88714478=	NC_000011.10:g.88714478G>C
GRCh37.p13 chr 11	NC_000011.9:g.88447646=	NC_000011.9:g.88447646G>C
GRM5 RefSeqGene	NG_052831.1:g.356494=	NG_052831.1:g.356494C>G
GRM5 transcript variant b	NM_000842.3:c.912-61075=	NM_000842.3:c.912-61075C>G
GRM5 transcript variant b	NM_000842.5:c.912-61075=	NM_000842.5:c.912-61075C>G
GRM5 transcript variant a	NM_001143831.2:c.912-61075=	NM_001143831.2:c.912-61075C>G
GRM5 transcript variant a	NM_001143831.3:c.912-61075=	NM_001143831.3:c.912-61075C>G
GRM5 transcript variant c	NM_001384268.1:c.912-61075=	NM_001384268.1:c.912-61075C>G
GRM5 transcript variant X1	XM_005273956.1:c.912-61075=	XM_005273956.1:c.912-61075C>G
GRM5 transcript variant X2	XM_005273957.1:c.912-61075=	XM_005273957.1:c.912-61075C>G
GRM5 transcript variant X1	XM_011542792.2:c.912-61075=	XM_011542792.2:c.912-61075C>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#.

72 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2185981	Oct 23, 2000 (88)
2	PERLEGEN	ss23383079	Sep 20, 2004 (123)
3	ABI	ss38681060	Mar 13, 2006 (126)
4	AFFY	ss66495871	Nov 30, 2006 (127)
5	AFFY	ss76319099	Dec 06, 2007 (129)
6	KRIBB_YJKIM	ss81467348	Dec 15, 2007 (130)
7	BCMHGSC_JDW	ss88681775	Mar 24, 2008 (129)
8	HUMANGENOME_JCVI	ss97496596	Feb 06, 2009 (130)
9	1000GENOMES	ss110811048	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss119928373	Dec 01, 2009 (131)
11	ENSEMBL	ss132712767	Dec 01, 2009 (131)
12	ENSEMBL	ss142663073	Dec 01, 2009 (131)
13	AFFY	ss173245041	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss175223878	Jul 04, 2010 (132)
15	BUSHMAN	ss203007916	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss207735357	Jul 04, 2010 (132)
17	1000GENOMES	ss225372677	Jul 14, 2010 (132)
18	1000GENOMES	ss235653605	Jul 15, 2010 (132)
19	1000GENOMES	ss242265346	Jul 15, 2010 (132)
20	GMI	ss281104445	May 04, 2012 (137)
21	GMI	ss286424929	Apr 25, 2013 (138)
22	PJP	ss291093185	May 09, 2011 (134)
23	TISHKOFF	ss562721194	Apr 25, 2013 (138)
24	SSMP	ss658236386	Apr 25, 2013 (138)
25	EVA-GONL	ss988789203	Aug 21, 2014 (142)
26	JMKIDD_LAB	ss1077916528	Aug 21, 2014 (142)
27	1000GENOMES	ss1342312154	Aug 21, 2014 (142)
28	DDI	ss1426707118	Apr 01, 2015 (144)
29	EVA_GENOME_DK	ss1575852719	Apr 01, 2015 (144)
30	EVA_DECODE	ss1598452488	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1627123004	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1670117037	Apr 01, 2015 (144)
33	EVA_SVP	ss1713272402	Apr 01, 2015 (144)
34	WEILL_CORNELL_DGM	ss1932148006	Feb 12, 2016 (147)
35	JJLAB	ss2026817205	Sep 14, 2016 (149)
36	USC_VALOUEV	ss2155129057	Dec 20, 2016 (150)
37	HUMAN_LONGEVITY	ss2184409022	Dec 20, 2016 (150)
38	SYSTEMSBIOZJU	ss2627880815	Nov 08, 2017 (151)
39	GRF	ss2699427398	Nov 08, 2017 (151)
40	GNOMAD	ss2902608110	Nov 08, 2017 (151)
41	SWEGEN	ss3008514262	Nov 08, 2017 (151)
42	BIOINF_KMB_FNS_UNIBA	ss3027206475	Nov 08, 2017 (151)
43	CSHL	ss3349715594	Nov 08, 2017 (151)
44	URBANLAB	ss3649664294	Oct 12, 2018 (152)
45	EGCUT_WGS	ss3675839382	Jul 13, 2019 (153)
46	EVA_DECODE	ss3692288646	Jul 13, 2019 (153)
47	ACPOP	ss3738396839	Jul 13, 2019 (153)
48	EVA	ss3749612102	Jul 13, 2019 (153)
49	PACBIO	ss3787019727	Jul 13, 2019 (153)
50	PACBIO	ss3792150144	Jul 13, 2019 (153)
51	PACBIO	ss3797032511	Jul 13, 2019 (153)
52	KHV_HUMAN_GENOMES	ss3814943658	Jul 13, 2019 (153)
53	EVA	ss3832754582	Apr 26, 2020 (154)
54	EVA	ss3839935433	Apr 26, 2020 (154)
55	EVA	ss3845416151	Apr 26, 2020 (154)
56	SGDP_PRJ	ss3876793277	Apr 26, 2020 (154)
57	KRGDB	ss3925221158	Apr 26, 2020 (154)
58	KOGIC	ss3970440678	Apr 26, 2020 (154)
59	TOPMED	ss4894274014	Apr 26, 2021 (155)
60	TOMMO_GENOMICS	ss5203161589	Apr 26, 2021 (155)
61	1000G_HIGH_COVERAGE	ss5288331696	Oct 16, 2022 (156)
62	EVA	ss5401212477	Oct 16, 2022 (156)
63	HUGCELL_USP	ss5483393507	Oct 16, 2022 (156)
64	EVA	ss5510455409	Oct 16, 2022 (156)
65	1000G_HIGH_COVERAGE	ss5584509287	Oct 16, 2022 (156)
66	SANFORD_IMAGENETICS	ss5651739641	Oct 16, 2022 (156)
67	TOMMO_GENOMICS	ss5751404757	Oct 16, 2022 (156)
68	YY_MCH	ss5812635405	Oct 16, 2022 (156)
69	EVA	ss5837007041	Oct 16, 2022 (156)
70	EVA	ss5850078441	Oct 16, 2022 (156)
71	EVA	ss5921008714	Oct 16, 2022 (156)
72	EVA	ss5943061869	Oct 16, 2022 (156)
73	1000Genomes	NC_000011.9 - 88447646	Oct 12, 2018 (152)
74	1000Genomes_30x	NC_000011.10 - 88714478	Oct 16, 2022 (156)
75	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 88447646	Oct 12, 2018 (152)
76	Genetic variation in the Estonian population	NC_000011.9 - 88447646	Oct 12, 2018 (152)
77	The Danish reference pan genome	NC_000011.9 - 88447646	Apr 26, 2020 (154)
78	gnomAD - Genomes	NC_000011.10 - 88714478	Apr 26, 2021 (155)
79	Genome of the Netherlands Release 5	NC_000011.9 - 88447646	Apr 26, 2020 (154)
80	HapMap	NC_000011.10 - 88714478	Apr 26, 2020 (154)
81	KOREAN population from KRGDB	NC_000011.9 - 88447646	Apr 26, 2020 (154)
82	Korean Genome Project	NC_000011.10 - 88714478	Apr 26, 2020 (154)
83	Northern Sweden	NC_000011.9 - 88447646	Jul 13, 2019 (153)
84	Qatari	NC_000011.9 - 88447646	Apr 26, 2020 (154)
85	SGDP_PRJ	NC_000011.9 - 88447646	Apr 26, 2020 (154)
86	Siberian	NC_000011.9 - 88447646	Apr 26, 2020 (154)
87	8.3KJPN	NC_000011.9 - 88447646	Apr 26, 2021 (155)
88	14KJPN	NC_000011.10 - 88714478	Oct 16, 2022 (156)
89	TopMed	NC_000011.10 - 88714478	Apr 26, 2021 (155)
90	UK 10K study - Twins	NC_000011.9 - 88447646	Oct 12, 2018 (152)
91	A Vietnamese Genetic Variation Database	NC_000011.9 - 88447646	Jul 13, 2019 (153)
92	ALFA	NC_000011.10 - 88714478	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).

Associated ID	History Updated (Build)
rs16914655	Oct 08, 2004 (123)
rs58506994	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss66495871, ss76319099, ss88681775, ss110811048, ss119928373, ss173245041, ss175223878, ss203007916, ss207735357, ss281104445, ss286424929, ss291093185, ss1598452488, ss1713272402	NC_000011.8:88087293:G:C	NC_000011.10:88714477:G:C	(self)
54869924, 30458816, 21577630, 2666269, 13590154, 32398552, 11681704, 14189936, 28810257, 7645411, 61130896, 30458816, 6755124, ss225372677, ss235653605, ss242265346, ss562721194, ss658236386, ss988789203, ss1077916528, ss1342312154, ss1426707118, ss1575852719, ss1627123004, ss1670117037, ss1932148006, ss2026817205, ss2155129057, ss2627880815, ss2699427398, ss2902608110, ss3008514262, ss3349715594, ss3675839382, ss3738396839, ss3749612102, ss3787019727, ss3792150144, ss3797032511, ss3832754582, ss3839935433, ss3876793277, ss3925221158, ss5203161589, ss5401212477, ss5510455409, ss5651739641, ss5837007041, ss5943061869	NC_000011.9:88447645:G:C	NC_000011.10:88714477:G:C	(self)
72035222, 387251184, 660581, 26818679, 85241861, 109819670, 5399180906, ss2184409022, ss3027206475, ss3649664294, ss3692288646, ss3814943658, ss3845416151, ss3970440678, ss4894274014, ss5288331696, ss5483393507, ss5584509287, ss5751404757, ss5812635405, ss5850078441, ss5921008714	NC_000011.10:88714477:G:C	NC_000011.10:88714477:G:C	(self)
ss2185981, ss23383079, ss38681060, ss81467348, ss97496596, ss132712767, ss142663073	NT_167190.1:33753440:G:C	NC_000011.10:88714477:G: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 rs1391875

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

rs1391875