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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs139978243

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:120802734 (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=0.000004 (1/264690, TOPMED)
T=0.000008 (2/251348, GnomAD_exome)
T=0.000016 (3/183546, ALFA) (+ 6 more)
T=0.000025 (3/121206, ExAC)
T=0.00003 (2/78694, PAGE_STUDY)
T=0.00015 (2/13004, GO-ESP)
T=0.0005 (3/6404, 1000G_30x)
T=0.0004 (2/5008, 1000G)
T=0.0021 (7/3284, PRJNA289433)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GRIK4 : Missense 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 183668 C=0.999984 T=0.000016
European Sub 157720 C=0.999981 T=0.000019
African Sub 4326 C=1.0000 T=0.0000
African Others Sub 168 C=1.000 T=0.000
African American Sub 4158 C=1.0000 T=0.0000
Asian Sub 6294 C=1.0000 T=0.0000
East Asian Sub 4476 C=1.0000 T=0.0000
Other Asian Sub 1818 C=1.0000 T=0.0000
Latin American 1 Sub 796 C=1.000 T=0.000
Latin American 2 Sub 968 C=1.000 T=0.000
South Asian Sub 280 C=1.000 T=0.000
Other Sub 13284 C=1.00000 T=0.00000


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 C=0.999996 T=0.000004
gnomAD - Exomes Global Study-wide 251348 C=0.999992 T=0.000008
gnomAD - Exomes European Sub 135284 C=0.999993 T=0.000007
gnomAD - Exomes Asian Sub 49002 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34592 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 16254 C=0.99994 T=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10078 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6138 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 183546 C=0.999984 T=0.000016
Allele Frequency Aggregator European Sub 157616 C=0.999981 T=0.000019
Allele Frequency Aggregator Other Sub 13280 C=1.00000 T=0.00000
Allele Frequency Aggregator Asian Sub 6294 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 4312 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 968 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 796 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 280 C=1.000 T=0.000
ExAC Global Study-wide 121206 C=0.999975 T=0.000025
ExAC Europe Sub 73196 C=0.99999 T=0.00001
ExAC Asian Sub 25154 C=1.00000 T=0.00000
ExAC American Sub 11572 C=0.99991 T=0.00009
ExAC African Sub 10378 C=0.99990 T=0.00010
ExAC Other Sub 906 C=1.000 T=0.000
The PAGE Study Global Study-wide 78694 C=0.99997 T=0.00003
The PAGE Study AfricanAmerican Sub 32514 C=0.99994 T=0.00006
The PAGE Study Mexican Sub 10806 C=1.00000 T=0.00000
The PAGE Study Asian Sub 8318 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 C=1.0000 T=0.0000
The PAGE Study NativeHawaiian Sub 4532 C=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 C=1.0000 T=0.0000
The PAGE Study Dominican Sub 3828 C=1.0000 T=0.0000
The PAGE Study CentralAmerican Sub 2450 C=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 C=1.0000 T=0.0000
The PAGE Study NativeAmerican Sub 1260 C=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 13004 C=0.99985 T=0.00015
GO Exome Sequencing Project European American Sub 8598 C=0.9998 T=0.0002
GO Exome Sequencing Project African American Sub 4406 C=1.0000 T=0.0000
1000Genomes_30x Global Study-wide 6404 C=0.9995 T=0.0005
1000Genomes_30x African Sub 1786 C=0.9994 T=0.0006
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=0.998 T=0.002
1000Genomes Global Study-wide 5008 C=0.9996 T=0.0004
1000Genomes African Sub 1322 C=0.9992 T=0.0008
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=0.999 T=0.001
MxGDAR/Encodat-PGx Global Study-wide 3284 C=0.9979 T=0.0021
MxGDAR/Encodat-PGx MxGDAR Sub 3284 C=0.9979 T=0.0021
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.p14 chr 11 NC_000011.10:g.120802734C>T
GRCh37.p13 chr 11 NC_000011.9:g.120673443C>T
GRIK4 RefSeqGene (LRG_1012) NG_042194.1:g.295989C>T
Gene: GRIK4, glutamate ionotropic receptor kainate type subunit 4 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GRIK4 transcript variant 2 NM_014619.5:c.124C>T R [CGG] > W [TGG] Coding Sequence Variant
glutamate receptor ionotropic, kainate 4 isoform 1 precursor NP_055434.2:p.Arg42Trp R (Arg) > W (Trp) Missense Variant
GRIK4 transcript variant 3 NM_001282473.3:c.124C>T R [CGG] > W [TGG] Coding Sequence Variant
glutamate receptor ionotropic, kainate 4 isoform 2 precursor NP_001269402.1:p.Arg42Trp R (Arg) > W (Trp) Missense Variant
GRIK4 transcript variant 1 NM_001282470.3:c.124C>T R [CGG] > W [TGG] Coding Sequence Variant
glutamate receptor ionotropic, kainate 4 isoform 1 precursor NP_001269399.1:p.Arg42Trp R (Arg) > W (Trp) Missense Variant
GRIK4 transcript variant X5 XM_011542786.3:c. N/A Genic Upstream Transcript Variant
GRIK4 transcript variant X6 XM_011542787.3:c. N/A Genic Upstream Transcript Variant
GRIK4 transcript variant X4 XM_047426840.1:c. N/A Genic Upstream Transcript Variant
GRIK4 transcript variant X1 XM_011542784.3:c.124C>T R [CGG] > W [TGG] Coding Sequence Variant
glutamate receptor ionotropic, kainate 4 isoform X1 XP_011541086.1:p.Arg42Trp R (Arg) > W (Trp) Missense Variant
GRIK4 transcript variant X2 XM_017017621.3:c.124C>T R [CGG] > W [TGG] Coding Sequence Variant
glutamate receptor ionotropic, kainate 4 isoform X2 XP_016873110.1:p.Arg42Trp R (Arg) > W (Trp) Missense Variant
GRIK4 transcript variant X3 XM_017017622.3:c.124C>T R [CGG] > W [TGG] Coding Sequence Variant
glutamate receptor ionotropic, kainate 4 isoform X3 XP_016873111.1:p.Arg42Trp R (Arg) > W (Trp) Missense 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
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 C= T
GRCh38.p14 chr 11 NC_000011.10:g.120802734= NC_000011.10:g.120802734C>T
GRCh37.p13 chr 11 NC_000011.9:g.120673443= NC_000011.9:g.120673443C>T
GRIK4 RefSeqGene (LRG_1012) NG_042194.1:g.295989= NG_042194.1:g.295989C>T
GRIK4 transcript variant 2 NM_014619.5:c.124= NM_014619.5:c.124C>T
GRIK4 transcript variant 2 NM_014619.4:c.124= NM_014619.4:c.124C>T
GRIK4 transcript variant 2 NM_014619.3:c.124= NM_014619.3:c.124C>T
GRIK4 transcript NM_014619.2:c.124= NM_014619.2:c.124C>T
GRIK4 transcript variant 1 NM_001282470.3:c.124= NM_001282470.3:c.124C>T
GRIK4 transcript variant 1 NM_001282470.2:c.124= NM_001282470.2:c.124C>T
GRIK4 transcript variant 1 NM_001282470.1:c.124= NM_001282470.1:c.124C>T
GRIK4 transcript variant 3 NM_001282473.3:c.124= NM_001282473.3:c.124C>T
GRIK4 transcript variant 3 NM_001282473.2:c.124= NM_001282473.2:c.124C>T
GRIK4 transcript variant 3 NM_001282473.1:c.124= NM_001282473.1:c.124C>T
GRIK4 transcript variant X1 XM_011542784.3:c.124= XM_011542784.3:c.124C>T
GRIK4 transcript variant X1 XM_011542784.2:c.124= XM_011542784.2:c.124C>T
GRIK4 transcript variant X1 XM_011542784.1:c.124= XM_011542784.1:c.124C>T
GRIK4 transcript variant X2 XM_017017621.3:c.124= XM_017017621.3:c.124C>T
GRIK4 transcript variant X2 XM_017017621.2:c.124= XM_017017621.2:c.124C>T
GRIK4 transcript variant X2 XM_017017621.1:c.124= XM_017017621.1:c.124C>T
GRIK4 transcript variant X3 XM_017017622.3:c.124= XM_017017622.3:c.124C>T
GRIK4 transcript variant X3 XM_017017622.2:c.124= XM_017017622.2:c.124C>T
GRIK4 transcript variant X3 XM_017017622.1:c.124= XM_017017622.1:c.124C>T
glutamate receptor ionotropic, kainate 4 isoform 1 precursor NP_055434.2:p.Arg42= NP_055434.2:p.Arg42Trp
glutamate receptor ionotropic, kainate 4 isoform 1 precursor NP_001269399.1:p.Arg42= NP_001269399.1:p.Arg42Trp
glutamate receptor ionotropic, kainate 4 isoform 2 precursor NP_001269402.1:p.Arg42= NP_001269402.1:p.Arg42Trp
glutamate receptor ionotropic, kainate 4 isoform X1 XP_011541086.1:p.Arg42= XP_011541086.1:p.Arg42Trp
glutamate receptor ionotropic, kainate 4 isoform X2 XP_016873110.1:p.Arg42= XP_016873110.1:p.Arg42Trp
glutamate receptor ionotropic, kainate 4 isoform X3 XP_016873111.1:p.Arg42= XP_016873111.1:p.Arg42Trp
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#.

33 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342343030 May 09, 2011 (134)
2 1000GENOMES ss488979097 May 04, 2012 (137)
3 EXOME_CHIP ss491460520 May 04, 2012 (137)
4 ILLUMINA ss780905176 Sep 08, 2015 (146)
5 ILLUMINA ss783592489 Sep 08, 2015 (146)
6 1000GENOMES ss1343239383 Aug 21, 2014 (142)
7 EVA_EXAC ss1690678429 Apr 01, 2015 (144)
8 ILLUMINA ss1751999069 Sep 08, 2015 (146)
9 ILLUMINA ss1917867687 Feb 12, 2016 (147)
10 ILLUMINA ss1946325072 Feb 12, 2016 (147)
11 ILLUMINA ss1959393278 Feb 12, 2016 (147)
12 GNOMAD ss2739460032 Nov 08, 2017 (151)
13 ILLUMINA ss3021384196 Nov 08, 2017 (151)
14 ILLUMINA ss3626766783 Oct 12, 2018 (152)
15 ILLUMINA ss3634479514 Oct 12, 2018 (152)
16 ILLUMINA ss3640186850 Oct 12, 2018 (152)
17 ILLUMINA ss3644577956 Oct 12, 2018 (152)
18 ILLUMINA ss3651753415 Oct 12, 2018 (152)
19 ILLUMINA ss3725283679 Jul 13, 2019 (153)
20 ILLUMINA ss3744388759 Jul 13, 2019 (153)
21 ILLUMINA ss3744780272 Jul 13, 2019 (153)
22 PAGE_CC ss3771658545 Jul 13, 2019 (153)
23 ILLUMINA ss3772279991 Jul 13, 2019 (153)
24 EVA ss3824681126 Apr 26, 2020 (154)
25 EVA ss3984449446 Apr 26, 2021 (155)
26 TOPMED ss4902328709 Apr 26, 2021 (155)
27 1000G_HIGH_COVERAGE ss5289138115 Oct 16, 2022 (156)
28 EVA ss5402685273 Oct 16, 2022 (156)
29 1000G_HIGH_COVERAGE ss5585741106 Oct 16, 2022 (156)
30 EVA ss5847651300 Oct 16, 2022 (156)
31 EVA ss5921935338 Oct 16, 2022 (156)
32 EVA ss5943543198 Oct 16, 2022 (156)
33 EVA ss5979374486 Oct 16, 2022 (156)
34 1000Genomes NC_000011.9 - 120673443 Oct 12, 2018 (152)
35 1000Genomes_30x NC_000011.10 - 120802734 Oct 16, 2022 (156)
36 ExAC NC_000011.9 - 120673443 Oct 12, 2018 (152)
37 gnomAD - Exomes NC_000011.9 - 120673443 Jul 13, 2019 (153)
38 GO Exome Sequencing Project NC_000011.9 - 120673443 Oct 12, 2018 (152)
39 The PAGE Study NC_000011.10 - 120802734 Jul 13, 2019 (153)
40 MxGDAR/Encodat-PGx NC_000011.9 - 120673443 Apr 26, 2021 (155)
41 TopMed NC_000011.10 - 120802734 Apr 26, 2021 (155)
42 ALFA NC_000011.10 - 120802734 Apr 26, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
55831236, 957746, 8680924, 1138645, 2447, ss342343030, ss488979097, ss491460520, ss780905176, ss783592489, ss1343239383, ss1690678429, ss1751999069, ss1917867687, ss1946325072, ss1959393278, ss2739460032, ss3021384196, ss3626766783, ss3634479514, ss3640186850, ss3644577956, ss3651753415, ss3744388759, ss3744780272, ss3772279991, ss3824681126, ss3984449446, ss5402685273, ss5847651300, ss5943543198, ss5979374486 NC_000011.9:120673442:C:T NC_000011.10:120802733:C:T (self)
73267041, 880014, 117874365, 14274652923, ss3725283679, ss3771658545, ss4902328709, ss5289138115, ss5585741106, ss5921935338 NC_000011.10:120802733:C:T NC_000011.10:120802733:C: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 rs139978243

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.post761+d5e8e07