Name: rs1004362
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.

rs1004362

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr9:101628141 (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: C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.138358 (36622/264690, TOPMED)
T=0.127988 (17939/140162, GnomAD)
T=0.14382 (12283/85406, ALFA) (+ 18 more)
T=0.15921 (4499/28258, 14KJPN)
T=0.15990 (2680/16760, 8.3KJPN)
T=0.1443 (924/6404, 1000G_30x)
T=0.1466 (734/5008, 1000G)
T=0.0757 (339/4480, Estonian)
T=0.1650 (636/3854, ALSPAC)
T=0.1551 (575/3708, TWINSUK)
T=0.1925 (564/2930, KOREAN)
T=0.1861 (341/1832, Korea1K)
T=0.126 (126/998, GoNL)
T=0.092 (55/600, NorthernSweden)
T=0.154 (82/534, MGP)
T=0.095 (31/328, HapMap)
T=0.162 (35/216, Qatari)
T=0.257 (55/214, Vietnamese)
C=0.459 (78/170, SGDP_PRJ)
T=0.05 (2/40, GENOME_DK)
C=0.42 (5/12, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: GRIN3A : 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	85406	C=0.85618	T=0.14382
European	Sub	67664	C=0.85319	T=0.14681
African	Sub	5378	C=0.9059	T=0.0941
African Others	Sub	202	C=0.916	T=0.084
African American	Sub	5176	C=0.9055	T=0.0945
Asian	Sub	576	C=0.745	T=0.255
East Asian	Sub	462	C=0.758	T=0.242
Other Asian	Sub	114	C=0.693	T=0.307
Latin American 1	Sub	672	C=0.872	T=0.128
Latin American 2	Sub	5728	C=0.8631	T=0.1369
South Asian	Sub	178	C=0.865	T=0.135
Other	Sub	5210	C=0.8461	T=0.1539

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	C=0.861642	T=0.138358
gnomAD - Genomes	Global	Study-wide	140162	C=0.872012	T=0.127988
gnomAD - Genomes	European	Sub	75906	C=0.86305	T=0.13695
gnomAD - Genomes	African	Sub	42022	C=0.90805	T=0.09195
gnomAD - Genomes	American	Sub	13640	C=0.85411	T=0.14589
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.8203	T=0.1797
gnomAD - Genomes	East Asian	Sub	3124	C=0.7535	T=0.2465
gnomAD - Genomes	Other	Sub	2148	C=0.8496	T=0.1504
Allele Frequency Aggregator	Total	Global	85406	C=0.85618	T=0.14382
Allele Frequency Aggregator	European	Sub	67664	C=0.85319	T=0.14681
Allele Frequency Aggregator	Latin American 2	Sub	5728	C=0.8631	T=0.1369
Allele Frequency Aggregator	African	Sub	5378	C=0.9059	T=0.0941
Allele Frequency Aggregator	Other	Sub	5210	C=0.8461	T=0.1539
Allele Frequency Aggregator	Latin American 1	Sub	672	C=0.872	T=0.128
Allele Frequency Aggregator	Asian	Sub	576	C=0.745	T=0.255
Allele Frequency Aggregator	South Asian	Sub	178	C=0.865	T=0.135
14KJPN	JAPANESE	Study-wide	28258	C=0.84079	T=0.15921
8.3KJPN	JAPANESE	Study-wide	16760	C=0.84010	T=0.15990
1000Genomes_30x	Global	Study-wide	6404	C=0.8557	T=0.1443
1000Genomes_30x	African	Sub	1786	C=0.9289	T=0.0711
1000Genomes_30x	Europe	Sub	1266	C=0.8657	T=0.1343
1000Genomes_30x	South Asian	Sub	1202	C=0.8461	T=0.1539
1000Genomes_30x	East Asian	Sub	1170	C=0.7590	T=0.2410
1000Genomes_30x	American	Sub	980	C=0.837	T=0.163
1000Genomes	Global	Study-wide	5008	C=0.8534	T=0.1466
1000Genomes	African	Sub	1322	C=0.9281	T=0.0719
1000Genomes	East Asian	Sub	1008	C=0.7639	T=0.2361
1000Genomes	Europe	Sub	1006	C=0.8628	T=0.1372
1000Genomes	South Asian	Sub	978	C=0.845	T=0.155
1000Genomes	American	Sub	694	C=0.840	T=0.160
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9243	T=0.0757
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8350	T=0.1650
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8449	T=0.1551
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.8075	T=0.1925
Korean Genome Project	KOREAN	Study-wide	1832	C=0.8139	T=0.1861
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.874	T=0.126
Northern Sweden	ACPOP	Study-wide	600	C=0.908	T=0.092
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.846	T=0.154
HapMap	Global	Study-wide	328	C=0.905	T=0.095
HapMap	African	Sub	120	C=0.933	T=0.067
HapMap	American	Sub	120	C=0.908	T=0.092
HapMap	Asian	Sub	88	C=0.86	T=0.14
Qatari	Global	Study-wide	216	C=0.838	T=0.162
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.743	T=0.257
SGDP_PRJ	Global	Study-wide	170	C=0.459	T=0.541
The Danish reference pan genome	Danish	Study-wide	40	C=0.95	T=0.05
Siberian	Global	Study-wide	12	C=0.42	T=0.58

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 9	NC_000009.12:g.101628141C>T
GRCh37.p13 chr 9	NC_000009.11:g.104390423C>T

Gene: GRIN3A, glutamate ionotropic receptor NMDA type subunit 3A (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GRIN3A transcript	NM_133445.3:c.2498+115G>A	N/A	Intron Variant
GRIN3A transcript variant X1	XM_011518211.3:c.2498+115… XM_011518211.3:c.2498+115G>A	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	C=	T
GRCh38.p14 chr 9	NC_000009.12:g.101628141=	NC_000009.12:g.101628141C>T
GRCh37.p13 chr 9	NC_000009.11:g.104390423=	NC_000009.11:g.104390423C>T
GRIN3A transcript	NM_133445.2:c.2498+115=	NM_133445.2:c.2498+115G>A
GRIN3A transcript	NM_133445.3:c.2498+115=	NM_133445.3:c.2498+115G>A
GRIN3A transcript variant X1	XM_011518211.3:c.2498+115=	XM_011518211.3:c.2498+115G>A

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#.

83 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1465829	Oct 05, 2000 (86)
2	ABI	ss43740490	Mar 13, 2006 (126)
3	SI_EXO	ss76895909	Dec 06, 2007 (129)
4	BCMHGSC_JDW	ss94115020	Mar 25, 2008 (129)
5	1000GENOMES	ss108949009	Jan 23, 2009 (130)
6	ENSEMBL	ss144282618	Dec 01, 2009 (131)
7	ILLUMINA	ss159855563	Dec 01, 2009 (131)
8	COMPLETE_GENOMICS	ss166754588	Jul 04, 2010 (132)
9	BCM-HGSC-SUB	ss206736587	Jul 04, 2010 (132)
10	1000GENOMES	ss224367059	Jul 14, 2010 (132)
11	1000GENOMES	ss234907163	Jul 15, 2010 (132)
12	1000GENOMES	ss241665598	Jul 15, 2010 (132)
13	GMI	ss280336246	May 04, 2012 (137)
14	ILLUMINA	ss479166762	May 04, 2012 (137)
15	ILLUMINA	ss479168680	May 04, 2012 (137)
16	ILLUMINA	ss479488761	Sep 08, 2015 (146)
17	ILLUMINA	ss484384530	May 04, 2012 (137)
18	ILLUMINA	ss536569037	Sep 08, 2015 (146)
19	TISHKOFF	ss561529651	Apr 25, 2013 (138)
20	SSMP	ss656025513	Apr 25, 2013 (138)
21	ILLUMINA	ss779056953	Aug 21, 2014 (142)
22	ILLUMINA	ss782638573	Aug 21, 2014 (142)
23	ILLUMINA	ss783608067	Aug 21, 2014 (142)
24	ILLUMINA	ss831888719	Apr 01, 2015 (144)
25	ILLUMINA	ss834520030	Aug 21, 2014 (142)
26	EVA-GONL	ss986811224	Aug 21, 2014 (142)
27	1000GENOMES	ss1334826771	Aug 21, 2014 (142)
28	DDI	ss1431911592	Apr 01, 2015 (144)
29	EVA_GENOME_DK	ss1583192668	Apr 01, 2015 (144)
30	EVA_DECODE	ss1596447546	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1623224311	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1666218344	Apr 01, 2015 (144)
33	EVA_MGP	ss1711231834	Apr 01, 2015 (144)
34	WEILL_CORNELL_DGM	ss1930125240	Feb 12, 2016 (147)
35	GENOMED	ss1971269159	Jul 19, 2016 (147)
36	JJLAB	ss2025780557	Sep 14, 2016 (149)
37	USC_VALOUEV	ss2154009375	Dec 20, 2016 (150)
38	HUMAN_LONGEVITY	ss2313125857	Dec 20, 2016 (150)
39	SYSTEMSBIOZJU	ss2627358486	Nov 08, 2017 (151)
40	GRF	ss2709883640	Nov 08, 2017 (151)
41	GNOMAD	ss2881439253	Nov 08, 2017 (151)
42	SWEGEN	ss3005334224	Nov 08, 2017 (151)
43	BIOINF_KMB_FNS_UNIBA	ss3026671125	Nov 08, 2017 (151)
44	CSHL	ss3348783731	Nov 08, 2017 (151)
45	ILLUMINA	ss3630317893	Oct 12, 2018 (152)
46	ILLUMINA	ss3632786326	Oct 12, 2018 (152)
47	ILLUMINA	ss3633542036	Oct 12, 2018 (152)
48	ILLUMINA	ss3634270691	Oct 12, 2018 (152)
49	ILLUMINA	ss3636972728	Oct 12, 2018 (152)
50	ILLUMINA	ss3641245670	Oct 12, 2018 (152)
51	ILLUMINA	ss3641543679	Oct 12, 2018 (152)
52	OMUKHERJEE_ADBS	ss3646395820	Oct 12, 2018 (152)
53	EGCUT_WGS	ss3672869800	Jul 13, 2019 (153)
54	EVA_DECODE	ss3724439874	Jul 13, 2019 (153)
55	ACPOP	ss3736735759	Jul 13, 2019 (153)
56	EVA	ss3769492638	Jul 13, 2019 (153)
57	KHV_HUMAN_GENOMES	ss3812658181	Jul 13, 2019 (153)
58	EVA	ss3831776844	Apr 26, 2020 (154)
59	EVA	ss3839416590	Apr 26, 2020 (154)
60	EVA	ss3844880592	Apr 26, 2020 (154)
61	SGDP_PRJ	ss3872742143	Apr 26, 2020 (154)
62	KRGDB	ss3920581475	Apr 26, 2020 (154)
63	KOGIC	ss3966430170	Apr 26, 2020 (154)
64	FSA-LAB	ss3984424405	Apr 26, 2021 (155)
65	EVA	ss4017450058	Apr 26, 2021 (155)
66	TOPMED	ss4830141198	Apr 26, 2021 (155)
67	TOMMO_GENOMICS	ss5194586879	Apr 26, 2021 (155)
68	1000G_HIGH_COVERAGE	ss5281628373	Oct 13, 2022 (156)
69	EVA	ss5389244364	Oct 13, 2022 (156)
70	HUGCELL_USP	ss5477547964	Oct 13, 2022 (156)
71	EVA	ss5509791288	Oct 13, 2022 (156)
72	1000G_HIGH_COVERAGE	ss5574412266	Oct 13, 2022 (156)
73	EVA	ss5624186158	Oct 13, 2022 (156)
74	SANFORD_IMAGENETICS	ss5647951880	Oct 13, 2022 (156)
75	TOMMO_GENOMICS	ss5738910368	Oct 13, 2022 (156)
76	EVA	ss5799791281	Oct 13, 2022 (156)
77	EVA	ss5800153131	Oct 13, 2022 (156)
78	YY_MCH	ss5810865088	Oct 13, 2022 (156)
79	EVA	ss5829529351	Oct 13, 2022 (156)
80	EVA	ss5856867784	Oct 13, 2022 (156)
81	EVA	ss5917389859	Oct 13, 2022 (156)
82	EVA	ss5977145339	Oct 13, 2022 (156)
83	EVA	ss5980568892	Oct 13, 2022 (156)
84	1000Genomes	NC_000009.11 - 104390423	Oct 12, 2018 (152)
85	1000Genomes_30x	NC_000009.12 - 101628141	Oct 13, 2022 (156)
86	The Avon Longitudinal Study of Parents and Children	NC_000009.11 - 104390423	Oct 12, 2018 (152)
87	Genetic variation in the Estonian population	NC_000009.11 - 104390423	Oct 12, 2018 (152)
88	The Danish reference pan genome	NC_000009.11 - 104390423	Apr 26, 2020 (154)
89	gnomAD - Genomes	NC_000009.12 - 101628141	Apr 26, 2021 (155)
90	Genome of the Netherlands Release 5	NC_000009.11 - 104390423	Apr 26, 2020 (154)
91	HapMap	NC_000009.12 - 101628141	Apr 26, 2020 (154)
92	KOREAN population from KRGDB	NC_000009.11 - 104390423	Apr 26, 2020 (154)
93	Korean Genome Project	NC_000009.12 - 101628141	Apr 26, 2020 (154)
94	Medical Genome Project healthy controls from Spanish population	NC_000009.11 - 104390423	Apr 26, 2020 (154)
95	Northern Sweden	NC_000009.11 - 104390423	Jul 13, 2019 (153)
96	Qatari	NC_000009.11 - 104390423	Apr 26, 2020 (154)
97	SGDP_PRJ	NC_000009.11 - 104390423	Apr 26, 2020 (154)
98	Siberian	NC_000009.11 - 104390423	Apr 26, 2020 (154)
99	8.3KJPN	NC_000009.11 - 104390423	Apr 26, 2021 (155)
100	14KJPN	NC_000009.12 - 101628141	Oct 13, 2022 (156)
101	TopMed	NC_000009.12 - 101628141	Apr 26, 2021 (155)
102	UK 10K study - Twins	NC_000009.11 - 104390423	Oct 12, 2018 (152)
103	A Vietnamese Genetic Variation Database	NC_000009.11 - 104390423	Jul 13, 2019 (153)
104	ALFA	NC_000009.12 - 101628141	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)
rs386509128	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss94115020, ss108949009, ss166754588, ss206736587, ss280336246, ss479166762, ss1596447546	NC_000009.10:103430243:C:T	NC_000009.12:101628140:C:T	(self)
47121816, 26176344, 18608048, 9357605, 11680942, 27758869, 347594, 10020624, 12167170, 24759123, 6525729, 52556186, 26176344, 5813936, ss224367059, ss234907163, ss241665598, ss479168680, ss479488761, ss484384530, ss536569037, ss561529651, ss656025513, ss779056953, ss782638573, ss783608067, ss831888719, ss834520030, ss986811224, ss1334826771, ss1431911592, ss1583192668, ss1623224311, ss1666218344, ss1711231834, ss1930125240, ss1971269159, ss2025780557, ss2154009375, ss2627358486, ss2709883640, ss2881439253, ss3005334224, ss3348783731, ss3630317893, ss3632786326, ss3633542036, ss3634270691, ss3636972728, ss3641245670, ss3641543679, ss3646395820, ss3672869800, ss3736735759, ss3769492638, ss3831776844, ss3839416590, ss3872742143, ss3920581475, ss3984424405, ss4017450058, ss5194586879, ss5389244364, ss5509791288, ss5624186158, ss5647951880, ss5799791281, ss5800153131, ss5829529351, ss5977145339, ss5980568892	NC_000009.11:104390422:C:T	NC_000009.12:101628140:C:T	(self)
61938201, 333129544, 3881067, 22808171, 72747472, 667518759, 2618286271, ss2313125857, ss3026671125, ss3724439874, ss3812658181, ss3844880592, ss3966430170, ss4830141198, ss5281628373, ss5477547964, ss5574412266, ss5738910368, ss5810865088, ss5856867784, ss5917389859	NC_000009.12:101628140:C:T	NC_000009.12:101628140:C:T	(self)
ss76895909	NT_008470.18:11711627:C:T	NC_000009.12:101628140:C:T	(self)
ss1465829, ss43740490, ss144282618, ss159855563	NT_008470.19:33554954:C:T	NC_000009.12:101628140:C:T	(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 rs1004362

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

rs1004362