Name: rs147627109
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.

rs147627109

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:105980891 (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: T>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.005716 (1513/264690, TOPMED)
A=0.006375 (894/140238, GnomAD)
A=0.00007 (2/28258, 14KJPN) (+ 13 more)
A=0.00773 (146/18890, ALFA)
A=0.00012 (2/16758, 8.3KJPN)
A=0.0027 (17/6404, 1000G_30x)
A=0.0028 (14/5008, 1000G)
A=0.0069 (31/4480, Estonian)
A=0.0138 (53/3854, ALSPAC)
A=0.0108 (40/3708, TWINSUK)
A=0.011 (11/998, GoNL)
A=0.010 (6/600, NorthernSweden)
A=0.019 (4/216, Qatari)
A=0.05 (2/40, GENOME_DK)
T=0.5 (2/4, SGDP_PRJ)
A=0.5 (2/4, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: GRIA4 : Non Coding Transcript Variant
LOC124902743 : 2KB Upstream 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	T=0.99227	A=0.00773
European	Sub	14286	T=0.99055	A=0.00945
African	Sub	2946	T=0.9993	A=0.0007
African Others	Sub	114	T=1.000	A=0.000
African American	Sub	2832	T=0.9993	A=0.0007
Asian	Sub	112	T=1.000	A=0.000
East Asian	Sub	86	T=1.00	A=0.00
Other Asian	Sub	26	T=1.00	A=0.00
Latin American 1	Sub	146	T=0.986	A=0.014
Latin American 2	Sub	610	T=0.997	A=0.003
South Asian	Sub	98	T=1.00	A=0.00
Other	Sub	692	T=0.993	A=0.007

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	T=0.994284	A=0.005716
gnomAD - Genomes	Global	Study-wide	140238	T=0.993625	A=0.006375
gnomAD - Genomes	European	Sub	75946	T=0.99035	A=0.00965
gnomAD - Genomes	African	Sub	42038	T=0.99803	A=0.00197
gnomAD - Genomes	American	Sub	13650	T=0.99502	A=0.00498
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=1.0000	A=0.0000
gnomAD - Genomes	East Asian	Sub	3134	T=1.0000	A=0.0000
gnomAD - Genomes	Other	Sub	2148	T=0.9953	A=0.0047
14KJPN	JAPANESE	Study-wide	28258	T=0.99993	A=0.00007
Allele Frequency Aggregator	Total	Global	18890	T=0.99227	A=0.00773
Allele Frequency Aggregator	European	Sub	14286	T=0.99055	A=0.00945
Allele Frequency Aggregator	African	Sub	2946	T=0.9993	A=0.0007
Allele Frequency Aggregator	Other	Sub	692	T=0.993	A=0.007
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.997	A=0.003
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.986	A=0.014
Allele Frequency Aggregator	Asian	Sub	112	T=1.000	A=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=1.00	A=0.00
8.3KJPN	JAPANESE	Study-wide	16758	T=0.99988	A=0.00012
1000Genomes_30x	Global	Study-wide	6404	T=0.9973	A=0.0027
1000Genomes_30x	African	Sub	1786	T=0.9994	A=0.0006
1000Genomes_30x	Europe	Sub	1266	T=0.9945	A=0.0055
1000Genomes_30x	South Asian	Sub	1202	T=0.9975	A=0.0025
1000Genomes_30x	East Asian	Sub	1170	T=0.9991	A=0.0009
1000Genomes_30x	American	Sub	980	T=0.995	A=0.005
1000Genomes	Global	Study-wide	5008	T=0.9972	A=0.0028
1000Genomes	African	Sub	1322	T=0.9992	A=0.0008
1000Genomes	East Asian	Sub	1008	T=0.9990	A=0.0010
1000Genomes	Europe	Sub	1006	T=0.9930	A=0.0070
1000Genomes	South Asian	Sub	978	T=0.997	A=0.003
1000Genomes	American	Sub	694	T=0.997	A=0.003
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9931	A=0.0069
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9862	A=0.0138
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9892	A=0.0108
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.989	A=0.011
Northern Sweden	ACPOP	Study-wide	600	T=0.990	A=0.010
Qatari	Global	Study-wide	216	T=0.981	A=0.019
The Danish reference pan genome	Danish	Study-wide	40	T=0.95	A=0.05
SGDP_PRJ	Global	Study-wide	4	T=0.5	A=0.5

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.105980891T>A
GRCh37.p13 chr 11	NC_000011.9:g.105851618T>A

Gene: GRIA4, glutamate ionotropic receptor AMPA type subunit 4 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GRIA4 transcript variant 1	NM_000829.4:c.*1152=	N/A	3 Prime UTR Variant
GRIA4 transcript variant 2	NM_001077243.3:c.*1319=	N/A	3 Prime UTR Variant
GRIA4 transcript variant 3	NM_001077244.2:c.	N/A	Genic Downstream Transcript Variant
GRIA4 transcript variant 4	NM_001112812.2:c.	N/A	Genic Downstream Transcript Variant
GRIA4 transcript variant 5	NR_046356.2:n.4192T>A	N/A	Non Coding Transcript Variant
GRIA4 transcript variant X1	XM_006718823.3:c.*1152=	N/A	3 Prime UTR Variant
GRIA4 transcript variant X2	XM_005271518.4:c.*1152=	N/A	3 Prime UTR Variant
GRIA4 transcript variant X3	XM_047426831.1:c.*1152=	N/A	3 Prime UTR Variant
GRIA4 transcript variant X6	XM_011542777.4:c.*1152=	N/A	3 Prime UTR Variant
GRIA4 transcript variant X7	XM_017017611.3:c.*1152=	N/A	3 Prime UTR Variant
GRIA4 transcript variant X4	XM_017017609.2:c.	N/A	Genic Downstream Transcript Variant
GRIA4 transcript variant X5	XM_017017610.3:c.	N/A	Genic Downstream Transcript Variant
GRIA4 transcript variant X8	XM_024448454.2:c.	N/A	Genic Downstream Transcript Variant
GRIA4 transcript variant X9	XM_024448455.2:c.	N/A	Genic Downstream Transcript Variant

Gene: LOC124902743, uncharacterized LOC124902743 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124902743 transcript	XR_007062873.1:n.	N/A	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	T=	A
GRCh38.p14 chr 11	NC_000011.10:g.105980891=	NC_000011.10:g.105980891T>A
GRCh37.p13 chr 11	NC_000011.9:g.105851618=	NC_000011.9:g.105851618T>A
GRIA4 transcript variant X6	XM_011542777.4:c.*1152=	XM_011542777.4:c.*1152T>A
GRIA4 transcript variant X8	XM_011542777.2:c.*1152=	XM_011542777.2:c.*1152T>A
GRIA4 transcript variant X6	XM_011542777.1:c.*1152=	XM_011542777.1:c.*1152T>A
GRIA4 transcript variant X2	XM_005271518.4:c.*1152=	XM_005271518.4:c.*1152T>A
GRIA4 transcript variant X2	XM_005271518.2:c.*1152=	XM_005271518.2:c.*1152T>A
GRIA4 transcript variant X1	XM_005271518.1:c.*1152=	XM_005271518.1:c.*1152T>A
GRIA4 transcript variant 1	NM_000829.4:c.*1152=	NM_000829.4:c.*1152T>A
GRIA4 transcript variant 1	NM_000829.3:c.*1152=	NM_000829.3:c.*1152T>A
GRIA4 transcript variant X7	XM_017017611.3:c.*1152=	XM_017017611.3:c.*1152T>A
GRIA4 transcript variant X9	XM_017017611.1:c.*1152=	XM_017017611.1:c.*1152T>A
GRIA4 transcript variant 2	NM_001077243.3:c.*1319=	NM_001077243.3:c.*1319T>A
GRIA4 transcript variant 2	NM_001077243.2:c.*1319=	NM_001077243.2:c.*1319T>A
GRIA4 transcript variant X1	XM_006718823.3:c.*1152=	XM_006718823.3:c.*1152T>A
GRIA4 transcript variant X2	XM_006718823.1:c.*1152=	XM_006718823.1:c.*1152T>A
GRIA4 transcript variant 5	NR_046356.2:n.4192=	NR_046356.2:n.4192T>A
GRIA4 transcript variant 5	NR_046356.1:n.4214=	NR_046356.1:n.4214T>A
GRIA4 transcript variant X3	XM_047426831.1:c.*1152=	XM_047426831.1:c.*1152T>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#.

30 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss336963843	May 09, 2011 (134)
2	ILLUMINA	ss534831145	Sep 08, 2015 (146)
3	EVA-GONL	ss988924719	Aug 21, 2014 (142)
4	1000GENOMES	ss1342817233	Aug 21, 2014 (142)
5	EVA_GENOME_DK	ss1575932187	Apr 01, 2015 (144)
6	EVA_DECODE	ss1598589234	Apr 01, 2015 (144)
7	EVA_UK10K_ALSPAC	ss1627381697	Apr 01, 2015 (144)
8	EVA_UK10K_TWINSUK	ss1670375730	Apr 01, 2015 (144)
9	WEILL_CORNELL_DGM	ss1932287008	Feb 12, 2016 (147)
10	JJLAB	ss2026888195	Sep 14, 2016 (149)
11	HUMAN_LONGEVITY	ss2185392854	Dec 20, 2016 (150)
12	GNOMAD	ss2904036289	Nov 08, 2017 (151)
13	SWEGEN	ss3008721737	Nov 08, 2017 (151)
14	ILLUMINA	ss3626742331	Oct 12, 2018 (152)
15	EGCUT_WGS	ss3676044830	Jul 13, 2019 (153)
16	EVA_DECODE	ss3692528655	Jul 13, 2019 (153)
17	ACPOP	ss3738510613	Jul 13, 2019 (153)
18	EVA	ss3825808436	Apr 26, 2020 (154)
19	SGDP_PRJ	ss3877064473	Apr 26, 2020 (154)
20	TOPMED	ss4898658286	Apr 26, 2021 (155)
21	TOMMO_GENOMICS	ss5203725321	Apr 26, 2021 (155)
22	1000G_HIGH_COVERAGE	ss5288774187	Oct 16, 2022 (156)
23	EVA	ss5402006878	Oct 16, 2022 (156)
24	HUGCELL_USP	ss5483774874	Oct 16, 2022 (156)
25	1000G_HIGH_COVERAGE	ss5585192932	Oct 16, 2022 (156)
26	SANFORD_IMAGENETICS	ss5652000755	Oct 16, 2022 (156)
27	TOMMO_GENOMICS	ss5752124597	Oct 16, 2022 (156)
28	EVA	ss5837178788	Oct 16, 2022 (156)
29	EVA	ss5921507046	Oct 16, 2022 (156)
30	EVA	ss5943325023	Oct 16, 2022 (156)
31	1000Genomes	NC_000011.9 - 105851618	Oct 12, 2018 (152)
32	1000Genomes_30x	NC_000011.10 - 105980891	Oct 16, 2022 (156)
33	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 105851618	Oct 12, 2018 (152)
34	Genetic variation in the Estonian population	NC_000011.9 - 105851618	Oct 12, 2018 (152)
35	The Danish reference pan genome	NC_000011.9 - 105851618	Apr 26, 2020 (154)
36	gnomAD - Genomes	NC_000011.10 - 105980891	Apr 26, 2021 (155)
37	Genome of the Netherlands Release 5	NC_000011.9 - 105851618	Apr 26, 2020 (154)
38	Northern Sweden	NC_000011.9 - 105851618	Jul 13, 2019 (153)
39	Qatari	NC_000011.9 - 105851618	Apr 26, 2020 (154)
40	SGDP_PRJ	NC_000011.9 - 105851618	Apr 26, 2020 (154)
41	8.3KJPN	NC_000011.9 - 105851618	Apr 26, 2021 (155)
42	14KJPN	NC_000011.10 - 105980891	Oct 16, 2022 (156)
43	TopMed	NC_000011.10 - 105980891	Apr 26, 2021 (155)
44	UK 10K study - Twins	NC_000011.9 - 105851618	Oct 12, 2018 (152)
45	ALFA	NC_000011.10 - 105980891	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1598589234	NC_000011.8:105356827:T:A	NC_000011.10:105980890:T:A	(self)
55393940, 30743024, 21783078, 2721719, 13722488, 11795478, 14328938, 29081453, 61694628, 30743024, ss336963843, ss534831145, ss988924719, ss1342817233, ss1575932187, ss1627381697, ss1670375730, ss1932287008, ss2026888195, ss2904036289, ss3008721737, ss3626742331, ss3676044830, ss3738510613, ss3825808436, ss3877064473, ss5203725321, ss5402006878, ss5652000755, ss5837178788, ss5943325023	NC_000011.9:105851617:T:A	NC_000011.10:105980890:T:A	(self)
72718867, 390883807, 85961701, 114203942, 6855227372, ss2185392854, ss3692528655, ss4898658286, ss5288774187, ss5483774874, ss5585192932, ss5752124597, ss5921507046	NC_000011.10:105980890:T:A	NC_000011.10:105980890:T:A	(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 rs147627109

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

rs147627109