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dbSNP Short Genetic Variations

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.

rs1290

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr12:66452946 (GRCh38.p13) 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=0.222026 (58768/264690, TOPMED)
T=0.227110 (31795/139998, GnomAD)
T=0.24648 (4656/18890, ALFA) (+ 14 more)
T=0.31987 (5361/16760, 8.3KJPN)
T=0.2111 (1057/5008, 1000G)
T=0.2645 (1185/4480, Estonian)
T=0.2753 (1061/3854, ALSPAC)
T=0.2829 (1049/3708, TWINSUK)
T=0.2734 (801/2930, KOREAN)
T=0.2718 (498/1832, Korea1K)
T=0.281 (280/998, GoNL)
T=0.228 (137/600, NorthernSweden)
G=0.420 (95/226, SGDP_PRJ)
T=0.301 (65/216, Qatari)
T=0.140 (30/214, Vietnamese)
T=0.23 (9/40, GENOME_DK)
G=0.47 (14/30, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GRIP1 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
Help

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.p13 chr 12 NC_000012.12:g.66452946G>A
GRCh38.p13 chr 12 NC_000012.12:g.66452946G>T
GRCh37.p13 chr 12 NC_000012.11:g.66846726G>A
GRCh37.p13 chr 12 NC_000012.11:g.66846726G>T
GRIP1 RefSeqGene NG_021400.2:g.621320C>T
GRIP1 RefSeqGene NG_021400.2:g.621320C>A
Gene: GRIP1, glutamate receptor interacting protein 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GRIP1 transcript variant 2 NM_001178074.2:c.1198+246…

NM_001178074.2:c.1198+2463C>T

N/A Intron Variant
GRIP1 transcript variant 3 NM_001366722.1:c.1354+246…

NM_001366722.1:c.1354+2463C>T

N/A Intron Variant
GRIP1 transcript variant 4 NM_001366723.1:c.1273+246…

NM_001366723.1:c.1273+2463C>T

N/A Intron Variant
GRIP1 transcript variant 5 NM_001366724.1:c.1276+246…

NM_001366724.1:c.1276+2463C>T

N/A Intron Variant
GRIP1 transcript variant 6 NM_001379345.1:c.1432+246…

NM_001379345.1:c.1432+2463C>T

N/A Intron Variant
GRIP1 transcript variant 7 NM_001379346.1:c.1354+246…

NM_001379346.1:c.1354+2463C>T

N/A Intron Variant
GRIP1 transcript variant 8 NM_001379347.1:c.1276+246…

NM_001379347.1:c.1276+2463C>T

N/A Intron Variant
GRIP1 transcript variant 9 NM_001379348.1:c.1273+246…

NM_001379348.1:c.1273+2463C>T

N/A Intron Variant
GRIP1 transcript variant 10 NM_001379349.1:c.1201+246…

NM_001379349.1:c.1201+2463C>T

N/A Intron Variant
GRIP1 transcript variant 11 NM_001379351.1:c.1198+246…

NM_001379351.1:c.1198+2463C>T

N/A Intron Variant
GRIP1 transcript variant 1 NM_021150.4:c.1198+2463C>T N/A Intron Variant
GRIP1 transcript variant X4 XM_005268754.4:c.1357+246…

XM_005268754.4:c.1357+2463C>T

N/A Intron Variant
GRIP1 transcript variant X6 XM_005268757.4:c.1276+246…

XM_005268757.4:c.1276+2463C>T

N/A Intron Variant
GRIP1 transcript variant X1 XM_017019098.1:c.1579+246…

XM_017019098.1:c.1579+2463C>T

N/A Intron Variant
GRIP1 transcript variant X3 XM_017019100.1:c.1423+246…

XM_017019100.1:c.1423+2463C>T

N/A Intron Variant
Help

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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 G=0.75352 T=0.24648
European Sub 14286 G=0.72589 T=0.27411
African Sub 2946 G=0.8792 T=0.1208
African Others Sub 114 G=0.930 T=0.070
African American Sub 2832 G=0.8771 T=0.1229
Asian Sub 112 G=0.777 T=0.223
East Asian Sub 86 G=0.76 T=0.24
Other Asian Sub 26 G=0.85 T=0.15
Latin American 1 Sub 146 G=0.685 T=0.315
Latin American 2 Sub 610 G=0.800 T=0.200
South Asian Sub 98 G=0.76 T=0.24
Other Sub 692 G=0.759 T=0.241


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.777974 T=0.222026
gnomAD - Genomes Global Study-wide 139998 G=0.772890 T=0.227110
gnomAD - Genomes European Sub 75798 G=0.72358 T=0.27642
gnomAD - Genomes African Sub 41960 G=0.87703 T=0.12297
gnomAD - Genomes American Sub 13646 G=0.77547 T=0.22453
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.5900 T=0.4100
gnomAD - Genomes East Asian Sub 3122 G=0.7726 T=0.2274
gnomAD - Genomes Other Sub 2148 G=0.7458 T=0.2542
8.3KJPN JAPANESE Study-wide 16760 G=0.68013 T=0.31987
1000Genomes Global Study-wide 5008 G=0.7889 T=0.2111
1000Genomes African Sub 1322 G=0.9009 T=0.0991
1000Genomes East Asian Sub 1008 G=0.7917 T=0.2083
1000Genomes Europe Sub 1006 G=0.6849 T=0.3151
1000Genomes South Asian Sub 978 G=0.726 T=0.274
1000Genomes American Sub 694 G=0.811 T=0.189
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7355 T=0.2645
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7247 T=0.2753
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7171 T=0.2829
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7266 A=0.0000, T=0.2734
Korean Genome Project KOREAN Study-wide 1832 G=0.7282 T=0.2718
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.719 T=0.281
Northern Sweden ACPOP Study-wide 600 G=0.772 T=0.228
SGDP_PRJ Global Study-wide 226 G=0.420 T=0.580
Qatari Global Study-wide 216 G=0.699 T=0.301
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.860 T=0.140
The Danish reference pan genome Danish Study-wide 40 G=0.78 T=0.23
Siberian Global Study-wide 30 G=0.47 T=0.53
Help

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.p13 chr 12 NC_000012.12:g.66452946= NC_000012.12:g.66452946G>A NC_000012.12:g.66452946G>T
GRCh37.p13 chr 12 NC_000012.11:g.66846726= NC_000012.11:g.66846726G>A NC_000012.11:g.66846726G>T
GRIP1 RefSeqGene NG_021400.2:g.621320= NG_021400.2:g.621320C>T NG_021400.2:g.621320C>A
GRIP1 transcript variant 2 NM_001178074.1:c.1198+2463= NM_001178074.1:c.1198+2463C>T NM_001178074.1:c.1198+2463C>A
GRIP1 transcript variant 2 NM_001178074.2:c.1198+2463= NM_001178074.2:c.1198+2463C>T NM_001178074.2:c.1198+2463C>A
GRIP1 transcript variant 3 NM_001366722.1:c.1354+2463= NM_001366722.1:c.1354+2463C>T NM_001366722.1:c.1354+2463C>A
GRIP1 transcript variant 4 NM_001366723.1:c.1273+2463= NM_001366723.1:c.1273+2463C>T NM_001366723.1:c.1273+2463C>A
GRIP1 transcript variant 5 NM_001366724.1:c.1276+2463= NM_001366724.1:c.1276+2463C>T NM_001366724.1:c.1276+2463C>A
GRIP1 transcript variant 6 NM_001379345.1:c.1432+2463= NM_001379345.1:c.1432+2463C>T NM_001379345.1:c.1432+2463C>A
GRIP1 transcript variant 7 NM_001379346.1:c.1354+2463= NM_001379346.1:c.1354+2463C>T NM_001379346.1:c.1354+2463C>A
GRIP1 transcript variant 8 NM_001379347.1:c.1276+2463= NM_001379347.1:c.1276+2463C>T NM_001379347.1:c.1276+2463C>A
GRIP1 transcript variant 9 NM_001379348.1:c.1273+2463= NM_001379348.1:c.1273+2463C>T NM_001379348.1:c.1273+2463C>A
GRIP1 transcript variant 10 NM_001379349.1:c.1201+2463= NM_001379349.1:c.1201+2463C>T NM_001379349.1:c.1201+2463C>A
GRIP1 transcript variant 11 NM_001379351.1:c.1198+2463= NM_001379351.1:c.1198+2463C>T NM_001379351.1:c.1198+2463C>A
GRIP1 transcript variant 1 NM_021150.3:c.1198+2463= NM_021150.3:c.1198+2463C>T NM_021150.3:c.1198+2463C>A
GRIP1 transcript variant 1 NM_021150.4:c.1198+2463= NM_021150.4:c.1198+2463C>T NM_021150.4:c.1198+2463C>A
GRIP1 transcript variant X1 XM_005268754.1:c.1357+2463= XM_005268754.1:c.1357+2463C>T XM_005268754.1:c.1357+2463C>A
GRIP1 transcript variant X4 XM_005268754.4:c.1357+2463= XM_005268754.4:c.1357+2463C>T XM_005268754.4:c.1357+2463C>A
GRIP1 transcript variant X2 XM_005268755.1:c.1354+2463= XM_005268755.1:c.1354+2463C>T XM_005268755.1:c.1354+2463C>A
GRIP1 transcript variant X3 XM_005268756.1:c.1357+2463= XM_005268756.1:c.1357+2463C>T XM_005268756.1:c.1357+2463C>A
GRIP1 transcript variant X4 XM_005268757.1:c.1276+2463= XM_005268757.1:c.1276+2463C>T XM_005268757.1:c.1276+2463C>A
GRIP1 transcript variant X6 XM_005268757.4:c.1276+2463= XM_005268757.4:c.1276+2463C>T XM_005268757.4:c.1276+2463C>A
GRIP1 transcript variant X5 XM_005268758.1:c.1201+2463= XM_005268758.1:c.1201+2463C>T XM_005268758.1:c.1201+2463C>A
GRIP1 transcript variant X6 XM_005268759.1:c.1201+2463= XM_005268759.1:c.1201+2463C>T XM_005268759.1:c.1201+2463C>A
GRIP1 transcript variant X1 XM_017019098.1:c.1579+2463= XM_017019098.1:c.1579+2463C>T XM_017019098.1:c.1579+2463C>A
GRIP1 transcript variant X3 XM_017019100.1:c.1423+2463= XM_017019100.1:c.1423+2463C>T XM_017019100.1:c.1423+2463C>A
Help

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#.

49 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 WIAF ss1315 Sep 19, 2000 (36)
2 YUSUKE ss4937306 Aug 28, 2002 (108)
3 BCM_SSAHASNP ss11056072 Jul 11, 2003 (116)
4 BGI ss106812684 Feb 05, 2009 (130)
5 1000GENOMES ss112082238 Jan 25, 2009 (130)
6 1000GENOMES ss113677043 Jan 25, 2009 (130)
7 COMPLETE_GENOMICS ss170111464 Jul 04, 2010 (132)
8 1000GENOMES ss225802648 Jul 14, 2010 (132)
9 1000GENOMES ss235970311 Jul 15, 2010 (132)
10 1000GENOMES ss242523848 Jul 15, 2010 (132)
11 GMI ss281436148 May 04, 2012 (137)
12 TISHKOFF ss563223775 Apr 25, 2013 (138)
13 SSMP ss658788374 Apr 25, 2013 (138)
14 EVA-GONL ss989637406 Aug 21, 2014 (142)
15 JMKIDD_LAB ss1078534977 Aug 21, 2014 (142)
16 1000GENOMES ss1345422873 Aug 21, 2014 (142)
17 DDI ss1426963159 Apr 01, 2015 (144)
18 EVA_GENOME_DK ss1576339953 Apr 01, 2015 (144)
19 EVA_DECODE ss1599314463 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1628798846 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1671792879 Apr 01, 2015 (144)
22 WEILL_CORNELL_DGM ss1933001395 Feb 12, 2016 (147)
23 JJLAB ss2027250038 Sep 14, 2016 (149)
24 USC_VALOUEV ss2155593046 Dec 20, 2016 (150)
25 HUMAN_LONGEVITY ss2190621979 Dec 20, 2016 (150)
26 TOPMED ss2354596182 Dec 20, 2016 (150)
27 SYSTEMSBIOZJU ss2628108074 Nov 08, 2017 (151)
28 GRF ss2699942486 Nov 08, 2017 (151)
29 GNOMAD ss2911691346 Nov 08, 2017 (151)
30 SWEGEN ss3009856596 Nov 08, 2017 (151)
31 BIOINF_KMB_FNS_UNIBA ss3027433956 Nov 08, 2017 (151)
32 TOPMED ss3173617017 Nov 08, 2017 (151)
33 CSHL ss3350109681 Nov 08, 2017 (151)
34 EGCUT_WGS ss3677125327 Jul 13, 2019 (153)
35 EVA_DECODE ss3693869047 Jul 13, 2019 (153)
36 ACPOP ss3739109264 Jul 13, 2019 (153)
37 EVA ss3750600796 Jul 13, 2019 (153)
38 PACBIO ss3787254178 Jul 13, 2019 (153)
39 PACBIO ss3792350862 Jul 13, 2019 (153)
40 PACBIO ss3797233695 Jul 13, 2019 (153)
41 KHV_HUMAN_GENOMES ss3815932547 Jul 13, 2019 (153)
42 EVA ss3833172141 Apr 27, 2020 (154)
43 EVA ss3840156054 Apr 27, 2020 (154)
44 EVA ss3845643026 Apr 27, 2020 (154)
45 SGDP_PRJ ss3878486082 Apr 27, 2020 (154)
46 KRGDB ss3927151258 Apr 27, 2020 (154)
47 KOGIC ss3972139862 Apr 27, 2020 (154)
48 TOPMED ss4921926014 Apr 27, 2021 (155)
49 TOMMO_GENOMICS ss5206792489 Apr 27, 2021 (155)
50 1000Genomes NC_000012.11 - 66846726 Oct 12, 2018 (152)
51 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 66846726 Oct 12, 2018 (152)
52 Genetic variation in the Estonian population NC_000012.11 - 66846726 Oct 12, 2018 (152)
53 The Danish reference pan genome NC_000012.11 - 66846726 Apr 27, 2020 (154)
54 gnomAD - Genomes NC_000012.12 - 66452946 Apr 27, 2021 (155)
55 Genome of the Netherlands Release 5 NC_000012.11 - 66846726 Apr 27, 2020 (154)
56 KOREAN population from KRGDB NC_000012.11 - 66846726 Apr 27, 2020 (154)
57 Korean Genome Project NC_000012.12 - 66452946 Apr 27, 2020 (154)
58 Northern Sweden NC_000012.11 - 66846726 Jul 13, 2019 (153)
59 Qatari NC_000012.11 - 66846726 Apr 27, 2020 (154)
60 SGDP_PRJ NC_000012.11 - 66846726 Apr 27, 2020 (154)
61 Siberian NC_000012.11 - 66846726 Apr 27, 2020 (154)
62 8.3KJPN NC_000012.11 - 66846726 Apr 27, 2021 (155)
63 TopMed NC_000012.12 - 66452946 Apr 27, 2021 (155)
64 UK 10K study - Twins NC_000012.11 - 66846726 Oct 12, 2018 (152)
65 A Vietnamese Genetic Variation Database NC_000012.11 - 66846726 Jul 13, 2019 (153)
66 ALFA NC_000012.12 - 66452946 Apr 27, 2021 (155)
Help

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)
rs3751279 Oct 08, 2002 (108)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
34328652, ss3927151258 NC_000012.11:66846725:G:A NC_000012.12:66452945:G:A (self)
ss112082238, ss113677043, ss170111464, ss281436148, ss1599314463 NC_000012.10:65132992:G:T NC_000012.12:66452945:G:T (self)
58186830, 32304397, 22863575, 3002201, 14413719, 34328652, 12394129, 15043325, 30503062, 8109400, 64761796, 32304397, 7169529, ss225802648, ss235970311, ss242523848, ss563223775, ss658788374, ss989637406, ss1078534977, ss1345422873, ss1426963159, ss1576339953, ss1628798846, ss1671792879, ss1933001395, ss2027250038, ss2155593046, ss2354596182, ss2628108074, ss2699942486, ss2911691346, ss3009856596, ss3350109681, ss3677125327, ss3739109264, ss3750600796, ss3787254178, ss3792350862, ss3797233695, ss3833172141, ss3840156054, ss3878486082, ss3927151258, ss5206792489 NC_000012.11:66846725:G:T NC_000012.12:66452945:G:T (self)
410361151, 28517863, 86040964, 137471671, 11761702843, ss2190621979, ss3027433956, ss3173617017, ss3693869047, ss3815932547, ss3845643026, ss3972139862, ss4921926014 NC_000012.12:66452945:G:T NC_000012.12:66452945:G:T (self)
ss11056072 NT_029419.10:28990031:G:T NC_000012.12:66452945:G:T (self)
ss1315, ss4937306, ss106812684 NT_029419.12:28990031:G:T NC_000012.12:66452945:G:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1290

Help

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.

Software version is: 2.0.1.post596+ae089ad