Name: rs7251496
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.

rs7251496

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:1006926 (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>A / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.406090 (107488/264690, TOPMED)
T=0.16800 (4747/28256, 14KJPN)
T=0.16661 (2792/16758, 8.3KJPN) (+ 16 more)
T=0.31205 (5079/16276, ALFA)
T=0.3620 (2318/6404, 1000G_30x)
T=0.3548 (1777/5008, 1000G)
T=0.4228 (1894/4480, Estonian)
T=0.3913 (1508/3854, ALSPAC)
T=0.3883 (1440/3708, TWINSUK)
T=0.1417 (414/2922, KOREAN)
T=0.1376 (252/1832, Korea1K)
T=0.3954 (673/1702, HapMap)
T=0.377 (376/998, GoNL)
T=0.385 (231/600, NorthernSweden)
G=0.421 (112/266, SGDP_PRJ)
T=0.403 (87/216, Qatari)
T=0.224 (48/214, Vietnamese)
T=0.30 (12/40, GENOME_DK)
G=0.39 (14/36, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: GRIN3B : 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	16276	G=0.68795	A=0.00000, T=0.31205
European	Sub	13288	G=0.67956	A=0.00000, T=0.32044
African	Sub	1874	G=0.6361	A=0.0000, T=0.3639
African Others	Sub	62	G=0.73	A=0.00, T=0.27
African American	Sub	1812	G=0.6330	A=0.0000, T=0.3670
Asian	Sub	86	G=0.95	A=0.00, T=0.05
East Asian	Sub	66	G=0.97	A=0.00, T=0.03
Other Asian	Sub	20	G=0.90	A=0.00, T=0.10
Latin American 1	Sub	94	G=0.95	A=0.00, T=0.05
Latin American 2	Sub	348	G=0.954	A=0.000, T=0.046
South Asian	Sub	58	G=0.98	A=0.00, T=0.02
Other	Sub	528	G=0.786	A=0.000, T=0.214

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=0.593910	T=0.406090
14KJPN	JAPANESE	Study-wide	28256	G=0.83200	T=0.16800
8.3KJPN	JAPANESE	Study-wide	16758	G=0.83339	T=0.16661
Allele Frequency Aggregator	Total	Global	16276	G=0.68795	A=0.00000, T=0.31205
Allele Frequency Aggregator	European	Sub	13288	G=0.67956	A=0.00000, T=0.32044
Allele Frequency Aggregator	African	Sub	1874	G=0.6361	A=0.0000, T=0.3639
Allele Frequency Aggregator	Other	Sub	528	G=0.786	A=0.000, T=0.214
Allele Frequency Aggregator	Latin American 2	Sub	348	G=0.954	A=0.000, T=0.046
Allele Frequency Aggregator	Latin American 1	Sub	94	G=0.95	A=0.00, T=0.05
Allele Frequency Aggregator	Asian	Sub	86	G=0.95	A=0.00, T=0.05
Allele Frequency Aggregator	South Asian	Sub	58	G=0.98	A=0.00, T=0.02
1000Genomes_30x	Global	Study-wide	6404	G=0.6380	T=0.3620
1000Genomes_30x	African	Sub	1786	G=0.4513	T=0.5487
1000Genomes_30x	Europe	Sub	1266	G=0.6098	T=0.3902
1000Genomes_30x	South Asian	Sub	1202	G=0.6714	T=0.3286
1000Genomes_30x	East Asian	Sub	1170	G=0.8274	T=0.1726
1000Genomes_30x	American	Sub	980	G=0.748	T=0.252
1000Genomes	Global	Study-wide	5008	G=0.6452	T=0.3548
1000Genomes	African	Sub	1322	G=0.4584	T=0.5416
1000Genomes	East Asian	Sub	1008	G=0.8323	T=0.1677
1000Genomes	Europe	Sub	1006	G=0.6123	T=0.3877
1000Genomes	South Asian	Sub	978	G=0.666	T=0.334
1000Genomes	American	Sub	694	G=0.748	T=0.252
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.5772	T=0.4228
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.6087	T=0.3913
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.6117	T=0.3883
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.8576	A=0.0007, T=0.1417
Korean Genome Project	KOREAN	Study-wide	1832	G=0.8624	T=0.1376
HapMap	Global	Study-wide	1702	G=0.6046	T=0.3954
HapMap	American	Sub	762	G=0.654	T=0.346
HapMap	African	Sub	684	G=0.500	T=0.500
HapMap	Europe	Sub	174	G=0.649	T=0.351
HapMap	Asian	Sub	82	G=0.93	T=0.07
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.623	T=0.377
Northern Sweden	ACPOP	Study-wide	600	G=0.615	T=0.385
SGDP_PRJ	Global	Study-wide	266	G=0.421	T=0.579
Qatari	Global	Study-wide	216	G=0.597	T=0.403
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.776	T=0.224
The Danish reference pan genome	Danish	Study-wide	40	G=0.70	T=0.30
Siberian	Global	Study-wide	36	G=0.39	T=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 19	NC_000019.10:g.1006926G>A
GRCh38.p14 chr 19	NC_000019.10:g.1006926G>T
GRCh37.p13 chr 19	NC_000019.9:g.1006925G>A
GRCh37.p13 chr 19	NC_000019.9:g.1006925G>T

Gene: GRIN3B, glutamate ionotropic receptor NMDA type subunit 3B (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GRIN3B transcript	NM_138690.3:c.2053-702G>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	G=	A	T
GRCh38.p14 chr 19	NC_000019.10:g.1006926=	NC_000019.10:g.1006926G>A	NC_000019.10:g.1006926G>T
GRCh37.p13 chr 19	NC_000019.9:g.1006925=	NC_000019.9:g.1006925G>A	NC_000019.9:g.1006925G>T
GRIN3B transcript	NM_138690.1:c.2053-702=	NM_138690.1:c.2053-702G>A	NM_138690.1:c.2053-702G>T
GRIN3B transcript	NM_138690.3:c.2053-702=	NM_138690.3:c.2053-702G>A	NM_138690.3:c.2053-702G>T

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#.

74 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss10928728	Jul 11, 2003 (116)
2	WI_SSAHASNP	ss14307909	Dec 05, 2003 (119)
3	CSHL-HAPMAP	ss16790760	Feb 27, 2004 (120)
4	CSHL-HAPMAP	ss19397791	Feb 27, 2004 (120)
5	ILLUMINA	ss75021593	Dec 06, 2007 (129)
6	HGSV	ss81298467	Dec 16, 2007 (130)
7	1000GENOMES	ss110973215	Jan 25, 2009 (130)
8	1000GENOMES	ss114731515	Jan 25, 2009 (130)
9	ILLUMINA-UK	ss117615427	Feb 14, 2009 (130)
10	KRIBB_YJKIM	ss119549183	Dec 01, 2009 (131)
11	COMPLETE_GENOMICS	ss167640154	Jul 04, 2010 (132)
12	COMPLETE_GENOMICS	ss168850162	Jul 04, 2010 (132)
13	ILLUMINA	ss174310256	Jul 04, 2010 (132)
14	BUSHMAN	ss203577899	Jul 04, 2010 (132)
15	BCM-HGSC-SUB	ss208453495	Jul 04, 2010 (132)
16	1000GENOMES	ss228005072	Jul 14, 2010 (132)
17	1000GENOMES	ss237575731	Jul 15, 2010 (132)
18	1000GENOMES	ss243803363	Jul 15, 2010 (132)
19	GMI	ss283095248	May 04, 2012 (137)
20	ILLUMINA	ss537456536	Sep 08, 2015 (146)
21	TISHKOFF	ss565803760	Apr 25, 2013 (138)
22	SSMP	ss661655579	Apr 25, 2013 (138)
23	EVA-GONL	ss994004426	Aug 21, 2014 (142)
24	JMKIDD_LAB	ss1081707204	Aug 21, 2014 (142)
25	1000GENOMES	ss1362032441	Aug 21, 2014 (142)
26	DDI	ss1428309317	Apr 01, 2015 (144)
27	EVA_GENOME_DK	ss1578522587	Apr 01, 2015 (144)
28	EVA_UK10K_ALSPAC	ss1637417804	Apr 01, 2015 (144)
29	EVA_UK10K_TWINSUK	ss1680411837	Apr 01, 2015 (144)
30	EVA_DECODE	ss1698067283	Apr 01, 2015 (144)
31	EVA_SVP	ss1713646345	Apr 01, 2015 (144)
32	HAMMER_LAB	ss1809169654	Sep 08, 2015 (146)
33	WEILL_CORNELL_DGM	ss1937480590	Feb 12, 2016 (147)
34	JJLAB	ss2029516055	Sep 14, 2016 (149)
35	USC_VALOUEV	ss2158026800	Dec 20, 2016 (150)
36	HUMAN_LONGEVITY	ss2223641132	Dec 20, 2016 (150)
37	GRF	ss2702630900	Nov 08, 2017 (151)
38	GNOMAD	ss2959508395	Nov 08, 2017 (151)
39	SWEGEN	ss3016947465	Nov 08, 2017 (151)
40	BIOINF_KMB_FNS_UNIBA	ss3028590657	Nov 08, 2017 (151)
41	CSHL	ss3352156788	Nov 08, 2017 (151)
42	ILLUMINA	ss3627869888	Oct 12, 2018 (152)
43	ILLUMINA	ss3638210694	Oct 12, 2018 (152)
44	ILLUMINA	ss3643185429	Oct 12, 2018 (152)
45	URBANLAB	ss3650850757	Oct 12, 2018 (152)
46	EGCUT_WGS	ss3683797234	Jul 13, 2019 (153)
47	EVA_DECODE	ss3702169524	Jul 13, 2019 (153)
48	ACPOP	ss3742780661	Jul 13, 2019 (153)
49	EVA	ss3755713732	Jul 13, 2019 (153)
50	PACBIO	ss3788444820	Jul 13, 2019 (153)
51	PACBIO	ss3793368425	Jul 13, 2019 (153)
52	PACBIO	ss3798255018	Jul 13, 2019 (153)
53	KHV_HUMAN_GENOMES	ss3820968106	Jul 13, 2019 (153)
54	EVA	ss3835307070	Apr 27, 2020 (154)
55	EVA	ss3841276264	Apr 27, 2020 (154)
56	EVA	ss3846780035	Apr 27, 2020 (154)
57	SGDP_PRJ	ss3887574773	Apr 27, 2020 (154)
58	KRGDB	ss3937496969	Apr 27, 2020 (154)
59	KOGIC	ss3980630886	Apr 27, 2020 (154)
60	TOPMED	ss5065337588	Apr 26, 2021 (155)
61	TOMMO_GENOMICS	ss5226319513	Apr 26, 2021 (155)
62	1000G_HIGH_COVERAGE	ss5306184520	Oct 16, 2022 (156)
63	EVA	ss5433046315	Oct 16, 2022 (156)
64	HUGCELL_USP	ss5498861560	Oct 16, 2022 (156)
65	EVA	ss5512027276	Oct 16, 2022 (156)
66	1000G_HIGH_COVERAGE	ss5611464247	Oct 16, 2022 (156)
67	SANFORD_IMAGENETICS	ss5661811034	Oct 16, 2022 (156)
68	TOMMO_GENOMICS	ss5784448504	Oct 16, 2022 (156)
69	YY_MCH	ss5817331575	Oct 16, 2022 (156)
70	EVA	ss5840136911	Oct 16, 2022 (156)
71	EVA	ss5852171821	Oct 16, 2022 (156)
72	EVA	ss5926979647	Oct 16, 2022 (156)
73	EVA	ss5953243677	Oct 16, 2022 (156)
74	EVA	ss5981022253	Oct 16, 2022 (156)
75	1000Genomes	NC_000019.9 - 1006925	Oct 12, 2018 (152)
76	1000Genomes_30x	NC_000019.10 - 1006926	Oct 16, 2022 (156)
77	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 1006925	Oct 12, 2018 (152)
78	Genetic variation in the Estonian population	NC_000019.9 - 1006925	Oct 12, 2018 (152)
79	The Danish reference pan genome	NC_000019.9 - 1006925	Apr 27, 2020 (154)
80	gnomAD - Genomes Submission ignored due to conflicting rows: Row 531705542 (NC_000019.10:1006925:G:A 1/140024) Row 531705543 (NC_000019.10:1006925:G:T 58776/139968)	-	Apr 26, 2021 (155)
81	gnomAD - Genomes Submission ignored due to conflicting rows: Row 531705542 (NC_000019.10:1006925:G:A 1/140024) Row 531705543 (NC_000019.10:1006925:G:T 58776/139968)	-	Apr 26, 2021 (155)
82	Genome of the Netherlands Release 5	NC_000019.9 - 1006925	Apr 27, 2020 (154)
83	HapMap	NC_000019.10 - 1006926	Apr 27, 2020 (154)
84	KOREAN population from KRGDB	NC_000019.9 - 1006925	Apr 27, 2020 (154)
85	Korean Genome Project	NC_000019.10 - 1006926	Apr 27, 2020 (154)
86	Northern Sweden	NC_000019.9 - 1006925	Jul 13, 2019 (153)
87	Qatari	NC_000019.9 - 1006925	Apr 27, 2020 (154)
88	SGDP_PRJ	NC_000019.9 - 1006925	Apr 27, 2020 (154)
89	Siberian	NC_000019.9 - 1006925	Apr 27, 2020 (154)
90	8.3KJPN	NC_000019.9 - 1006925	Apr 26, 2021 (155)
91	14KJPN	NC_000019.10 - 1006926	Oct 16, 2022 (156)
92	TopMed	NC_000019.10 - 1006926	Apr 26, 2021 (155)
93	UK 10K study - Twins	NC_000019.9 - 1006925	Oct 12, 2018 (152)
94	A Vietnamese Genetic Variation Database	NC_000019.9 - 1006925	Jul 13, 2019 (153)
95	ALFA	NC_000019.10 - 1006926	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)
rs61673148	May 27, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
44674363, ss3937496969	NC_000019.9:1006924:G:A	NC_000019.10:1006925:G:A	(self)
12863101534	NC_000019.10:1006925:G:A	NC_000019.10:1006925:G:A	(self)
ss81298467, ss110973215, ss114731515, ss117615427, ss167640154, ss168850162, ss203577899, ss208453495, ss283095248, ss1698067283, ss1713646345, ss3643185429	NC_000019.8:957924:G:T	NC_000019.10:1006925:G:T	(self)
75397729, 41795220, 29535482, 4709853, 18622254, 44674363, 16065526, 19522512, 39591753, 10543154, 84288820, 41795220, 9243553, ss228005072, ss237575731, ss243803363, ss537456536, ss565803760, ss661655579, ss994004426, ss1081707204, ss1362032441, ss1428309317, ss1578522587, ss1637417804, ss1680411837, ss1809169654, ss1937480590, ss2029516055, ss2158026800, ss2702630900, ss2959508395, ss3016947465, ss3352156788, ss3627869888, ss3638210694, ss3683797234, ss3742780661, ss3755713732, ss3788444820, ss3793368425, ss3798255018, ss3835307070, ss3841276264, ss3887574773, ss3937496969, ss5226319513, ss5433046315, ss5512027276, ss5661811034, ss5840136911, ss5953243677, ss5981022253	NC_000019.9:1006924:G:T	NC_000019.10:1006925:G:T	(self)
98990182, 1658023, 37008887, 118285608, 280883252, 12863101534, ss2223641132, ss3028590657, ss3650850757, ss3702169524, ss3820968106, ss3846780035, ss3980630886, ss5065337588, ss5306184520, ss5498861560, ss5611464247, ss5784448504, ss5817331575, ss5852171821, ss5926979647	NC_000019.10:1006925:G:T	NC_000019.10:1006925:G:T	(self)
ss10928728	NT_011255.13:946924:G:T	NC_000019.10:1006925:G:T	(self)
ss14307909, ss16790760, ss19397791, ss75021593, ss119549183, ss174310256	NT_011255.14:946924:G:T	NC_000019.10:1006925:G: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 rs7251496

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

rs7251496