Name: rs940245
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.

rs940245

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:6539392 (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: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.102195 (27050/264690, TOPMED)
A=0.101472 (14216/140098, GnomAD)
G=0.46553 (13155/28258, 14KJPN) (+ 17 more)
A=0.09942 (1878/18890, ALFA)
G=0.46408 (7777/16758, 8.3KJPN)
A=0.2113 (1353/6404, 1000G_30x)
A=0.2234 (1119/5008, 1000G)
A=0.1223 (548/4480, Estonian)
A=0.1038 (400/3854, ALSPAC)
A=0.1028 (381/3708, TWINSUK)
A=0.4915 (1440/2930, KOREAN)
A=0.4995 (915/1832, Korea1K)
A=0.094 (94/998, GoNL)
A=0.177 (106/600, NorthernSweden)
A=0.196 (101/516, SGDP_PRJ)
A=0.171 (37/216, Qatari)
A=0.433 (90/208, Vietnamese)
A=0.230 (47/204, HapMap)
A=0.17 (8/48, Siberian)
A=0.07 (3/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: GRID2IP : 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	A=0.09942	G=0.90058
European	Sub	14286	A=0.10661	G=0.89339
African	Sub	2946	A=0.0322	G=0.9678
African Others	Sub	114	A=0.026	G=0.974
African American	Sub	2832	A=0.0325	G=0.9675
Asian	Sub	112	A=0.482	G=0.518
East Asian	Sub	86	A=0.50	G=0.50
Other Asian	Sub	26	A=0.42	G=0.58
Latin American 1	Sub	146	A=0.103	G=0.897
Latin American 2	Sub	610	A=0.134	G=0.866
South Asian	Sub	98	A=0.30	G=0.70
Other	Sub	692	A=0.116	G=0.884

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	A=0.102195	G=0.897805
gnomAD - Genomes	Global	Study-wide	140098	A=0.101472	G=0.898528
gnomAD - Genomes	European	Sub	75888	A=0.11123	G=0.88877
gnomAD - Genomes	African	Sub	42000	A=0.04055	G=0.95945
gnomAD - Genomes	American	Sub	13610	A=0.12888	G=0.87112
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.2010	G=0.7990
gnomAD - Genomes	East Asian	Sub	3126	A=0.4424	G=0.5576
gnomAD - Genomes	Other	Sub	2150	A=0.1242	G=0.8758
14KJPN	JAPANESE	Study-wide	28258	A=0.53447	G=0.46553
Allele Frequency Aggregator	Total	Global	18890	A=0.09942	G=0.90058
Allele Frequency Aggregator	European	Sub	14286	A=0.10661	G=0.89339
Allele Frequency Aggregator	African	Sub	2946	A=0.0322	G=0.9678
Allele Frequency Aggregator	Other	Sub	692	A=0.116	G=0.884
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.134	G=0.866
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.103	G=0.897
Allele Frequency Aggregator	Asian	Sub	112	A=0.482	G=0.518
Allele Frequency Aggregator	South Asian	Sub	98	A=0.30	G=0.70
8.3KJPN	JAPANESE	Study-wide	16758	A=0.53592	G=0.46408
1000Genomes_30x	Global	Study-wide	6404	A=0.2113	G=0.7887
1000Genomes_30x	African	Sub	1786	A=0.0179	G=0.9821
1000Genomes_30x	Europe	Sub	1266	A=0.0948	G=0.9052
1000Genomes_30x	South Asian	Sub	1202	A=0.4434	G=0.5566
1000Genomes_30x	East Asian	Sub	1170	A=0.4444	G=0.5556
1000Genomes_30x	American	Sub	980	A=0.151	G=0.849
1000Genomes	Global	Study-wide	5008	A=0.2234	G=0.7766
1000Genomes	African	Sub	1322	A=0.0189	G=0.9811
1000Genomes	East Asian	Sub	1008	A=0.4514	G=0.5486
1000Genomes	Europe	Sub	1006	A=0.0954	G=0.9046
1000Genomes	South Asian	Sub	978	A=0.449	G=0.551
1000Genomes	American	Sub	694	A=0.150	G=0.850
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.1223	G=0.8777
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.1038	G=0.8962
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.1028	G=0.8972
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.4915	G=0.5085
Korean Genome Project	KOREAN	Study-wide	1832	A=0.4995	G=0.5005
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.094	G=0.906
Northern Sweden	ACPOP	Study-wide	600	A=0.177	G=0.823
SGDP_PRJ	Global	Study-wide	516	A=0.196	G=0.804
Qatari	Global	Study-wide	216	A=0.171	G=0.829
A Vietnamese Genetic Variation Database	Global	Study-wide	208	A=0.433	G=0.567
HapMap	Global	Study-wide	204	A=0.230	G=0.770
HapMap	African	Sub	118	A=0.008	G=0.992
HapMap	Asian	Sub	86	A=0.53	G=0.47
Siberian	Global	Study-wide	48	A=0.17	G=0.83
The Danish reference pan genome	Danish	Study-wide	40	A=0.07	G=0.93

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 7	NC_000007.14:g.6539392A>G
GRCh37.p13 chr 7	NC_000007.13:g.6579023A>G

Gene: GRID2IP, Grid2 interacting protein (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GRID2IP transcript variant 1	NM_001145118.2:c.584+326T… NM_001145118.2:c.584+326T>C	N/A	Intron Variant
GRID2IP transcript variant 2	NM_001388403.1:c.	N/A	Genic Upstream Transcript Variant
GRID2IP transcript variant 3	NM_001394781.1:c.	N/A	Genic Upstream Transcript Variant
GRID2IP transcript variant X1	XM_047420365.1: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	A=	G
GRCh38.p14 chr 7	NC_000007.14:g.6539392=	NC_000007.14:g.6539392A>G
GRCh37.p13 chr 7	NC_000007.13:g.6579023=	NC_000007.13:g.6579023A>G
GRID2IP transcript variant 1	NM_001145118.1:c.584+326=	NM_001145118.1:c.584+326T>C
GRID2IP transcript variant 1	NM_001145118.2:c.584+326=	NM_001145118.2:c.584+326T>C

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#.

79 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1380799	Oct 05, 2000 (86)
2	TSC-CSHL	ss5172046	Oct 08, 2002 (108)
3	SC_JCM	ss5698799	Feb 20, 2003 (111)
4	WI_SSAHASNP	ss6511746	Feb 20, 2003 (111)
5	WUGSC_SSAHASNP	ss14586146	Dec 05, 2003 (120)
6	SSAHASNP	ss22619274	Apr 05, 2004 (121)
7	ABI	ss42977985	Mar 15, 2006 (126)
8	HGSV	ss78415202	Dec 07, 2007 (129)
9	HGSV	ss83567977	Dec 15, 2007 (130)
10	HUMANGENOME_JCVI	ss98129428	Feb 05, 2009 (130)
11	BGI	ss104393954	Dec 01, 2009 (131)
12	1000GENOMES	ss111443361	Jan 25, 2009 (130)
13	1000GENOMES	ss113236884	Jan 25, 2009 (130)
14	ILLUMINA-UK	ss115904123	Dec 01, 2009 (131)
15	ENSEMBL	ss143759895	Dec 01, 2009 (131)
16	GMI	ss157987226	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss162007452	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss163581281	Jul 04, 2010 (132)
19	COMPLETE_GENOMICS	ss166083831	Jul 04, 2010 (132)
20	BUSHMAN	ss202877907	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss208363498	Jul 04, 2010 (132)
22	1000GENOMES	ss222876700	Jul 14, 2010 (132)
23	1000GENOMES	ss233827346	Jul 15, 2010 (132)
24	1000GENOMES	ss240812543	Jul 15, 2010 (132)
25	BL	ss254016363	May 09, 2011 (134)
26	GMI	ss279163599	May 04, 2012 (137)
27	GMI	ss285565730	Apr 25, 2013 (138)
28	PJP	ss293921328	May 09, 2011 (134)
29	TISHKOFF	ss559772747	Apr 25, 2013 (138)
30	SSMP	ss654119943	Apr 25, 2013 (138)
31	EVA-GONL	ss983891870	Aug 21, 2014 (142)
32	JMKIDD_LAB	ss1074316679	Aug 21, 2014 (142)
33	1000GENOMES	ss1323730756	Aug 21, 2014 (142)
34	DDI	ss1431010227	Apr 01, 2015 (144)
35	EVA_GENOME_DK	ss1582047259	Apr 01, 2015 (144)
36	EVA_DECODE	ss1593457588	Apr 01, 2015 (144)
37	EVA_UK10K_ALSPAC	ss1617468441	Apr 01, 2015 (144)
38	EVA_UK10K_TWINSUK	ss1660462474	Apr 01, 2015 (144)
39	HAMMER_LAB	ss1804842931	Sep 08, 2015 (146)
40	WEILL_CORNELL_DGM	ss1927136222	Feb 12, 2016 (147)
41	GENOMED	ss1970610063	Jul 19, 2016 (147)
42	JJLAB	ss2024237712	Sep 14, 2016 (149)
43	USC_VALOUEV	ss2152438172	Dec 20, 2016 (150)
44	HUMAN_LONGEVITY	ss2291354063	Dec 20, 2016 (150)
45	SYSTEMSBIOZJU	ss2626608290	Nov 08, 2017 (151)
46	GRF	ss2708087100	Nov 08, 2017 (151)
47	GNOMAD	ss2849219372	Nov 08, 2017 (151)
48	SWEGEN	ss3000545830	Nov 08, 2017 (151)
49	BIOINF_KMB_FNS_UNIBA	ss3025912570	Nov 08, 2017 (151)
50	CSHL	ss3347410552	Nov 08, 2017 (151)
51	URBANLAB	ss3648550480	Oct 12, 2018 (152)
52	EGCUT_WGS	ss3668468286	Jul 13, 2019 (153)
53	EVA_DECODE	ss3719006048	Jul 13, 2019 (153)
54	ACPOP	ss3734311116	Jul 13, 2019 (153)
55	EVA	ss3766127870	Jul 13, 2019 (153)
56	PACBIO	ss3785719417	Jul 13, 2019 (153)
57	PACBIO	ss3791035043	Jul 13, 2019 (153)
58	PACBIO	ss3795914758	Jul 13, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3809289259	Jul 13, 2019 (153)
60	EVA	ss3830385253	Apr 26, 2020 (154)
61	EVA	ss3838679285	Apr 26, 2020 (154)
62	EVA	ss3844129709	Apr 26, 2020 (154)
63	SGDP_PRJ	ss3866521029	Apr 26, 2020 (154)
64	KRGDB	ss3913547245	Apr 26, 2020 (154)
65	KOGIC	ss3960798098	Apr 26, 2020 (154)
66	TOPMED	ss4733936950	Apr 26, 2021 (155)
67	TOMMO_GENOMICS	ss5181602612	Apr 26, 2021 (155)
68	1000G_HIGH_COVERAGE	ss5271654411	Oct 13, 2022 (156)
69	EVA	ss5371346487	Oct 13, 2022 (156)
70	HUGCELL_USP	ss5468960081	Oct 13, 2022 (156)
71	1000G_HIGH_COVERAGE	ss5559205653	Oct 13, 2022 (156)
72	SANFORD_IMAGENETICS	ss5642237930	Oct 13, 2022 (156)
73	TOMMO_GENOMICS	ss5720998678	Oct 13, 2022 (156)
74	YY_MCH	ss5808288830	Oct 13, 2022 (156)
75	EVA	ss5822339744	Oct 13, 2022 (156)
76	EVA	ss5855739362	Oct 13, 2022 (156)
77	EVA	ss5857510279	Oct 13, 2022 (156)
78	EVA	ss5971428401	Oct 13, 2022 (156)
79	EVA	ss5980415243	Oct 13, 2022 (156)
80	1000Genomes	NC_000007.13 - 6579023	Oct 12, 2018 (152)
81	1000Genomes_30x	NC_000007.14 - 6539392	Oct 13, 2022 (156)
82	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 6579023	Oct 12, 2018 (152)
83	Genetic variation in the Estonian population	NC_000007.13 - 6579023	Oct 12, 2018 (152)
84	The Danish reference pan genome	NC_000007.13 - 6579023	Apr 26, 2020 (154)
85	gnomAD - Genomes	NC_000007.14 - 6539392	Apr 26, 2021 (155)
86	Genome of the Netherlands Release 5	NC_000007.13 - 6579023	Apr 26, 2020 (154)
87	HapMap	NC_000007.14 - 6539392	Apr 26, 2020 (154)
88	KOREAN population from KRGDB	NC_000007.13 - 6579023	Apr 26, 2020 (154)
89	Korean Genome Project	NC_000007.14 - 6539392	Apr 26, 2020 (154)
90	Northern Sweden	NC_000007.13 - 6579023	Jul 13, 2019 (153)
91	Qatari	NC_000007.13 - 6579023	Apr 26, 2020 (154)
92	SGDP_PRJ	NC_000007.13 - 6579023	Apr 26, 2020 (154)
93	Siberian	NC_000007.13 - 6579023	Apr 26, 2020 (154)
94	8.3KJPN	NC_000007.13 - 6579023	Apr 26, 2021 (155)
95	14KJPN	NC_000007.14 - 6539392	Oct 13, 2022 (156)
96	TopMed	NC_000007.14 - 6539392	Apr 26, 2021 (155)
97	UK 10K study - Twins	NC_000007.13 - 6579023	Oct 12, 2018 (152)
98	A Vietnamese Genetic Variation Database	NC_000007.13 - 6579023	Jul 13, 2019 (153)
99	ALFA	NC_000007.14 - 6539392	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)
rs10380572	Feb 27, 2004 (120)
rs59446946	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78415202, ss83567977	NC_000007.11:6352262:A:G	NC_000007.14:6539391:A:G	(self)
ss111443361, ss113236884, ss115904123, ss162007452, ss163581281, ss166083831, ss202877907, ss208363498, ss254016363, ss279163599, ss285565730, ss293921328, ss1593457588	NC_000007.12:6545547:A:G	NC_000007.14:6539391:A:G	(self)
35652184, 19875300, 14206534, 8212198, 8851378, 20724639, 7595981, 9178152, 18538009, 4954526, 39571919, 19875300, 4422879, ss222876700, ss233827346, ss240812543, ss559772747, ss654119943, ss983891870, ss1074316679, ss1323730756, ss1431010227, ss1582047259, ss1617468441, ss1660462474, ss1804842931, ss1927136222, ss1970610063, ss2024237712, ss2152438172, ss2626608290, ss2708087100, ss2849219372, ss3000545830, ss3347410552, ss3668468286, ss3734311116, ss3766127870, ss3785719417, ss3791035043, ss3795914758, ss3830385253, ss3838679285, ss3866521029, ss3913547245, ss5181602612, ss5371346487, ss5642237930, ss5822339744, ss5971428401, ss5980415243	NC_000007.13:6579022:A:G	NC_000007.14:6539391:A:G	(self)
46731588, 251514413, 3323486, 17176099, 54835782, 571314509, 5017682741, ss2291354063, ss3025912570, ss3648550480, ss3719006048, ss3809289259, ss3844129709, ss3960798098, ss4733936950, ss5271654411, ss5468960081, ss5559205653, ss5720998678, ss5808288830, ss5855739362, ss5857510279	NC_000007.14:6539391:A:G	NC_000007.14:6539391:A:G	(self)
ss14586146, ss22619274	NT_007819.14:5874695:A:G	NC_000007.14:6539391:A:G	(self)
ss1380799, ss5172046, ss5698799, ss6511746, ss42977985, ss98129428, ss104393954, ss143759895, ss157987226	NT_007819.17:6569022:A:G	NC_000007.14:6539391:A:G	(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 rs940245

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

rs940245