Name: rs3091274
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.

rs3091274

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:55164 (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>A / C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.12857 (9647/75034, GnomAD)
C=0.00014 (4/27826, 14KJPN)
C=0.00030 (5/16528, 8.3KJPN) (+ 9 more)
C=0.07073 (839/11862, ALFA)
C=0.0938 (601/6404, 1000G_30x)
C=0.0767 (384/5008, 1000G)
C=0.0010 (3/2874, KOREAN)
C=0.0022 (4/1808, Korea1K)
C=0.002 (2/998, GoNL)
C=0.036 (17/474, SGDP_PRJ)
C=0.105 (18/172, Qatari)
C=0.00 (0/38, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	11862	C=0.07073	A=0.92927
European	Sub	7618	C=0.0046	A=0.9954
African	Sub	2816	C=0.2603	A=0.7397
African Others	Sub	108	C=0.333	A=0.667
African American	Sub	2708	C=0.2574	A=0.7426
Asian	Sub	108	C=0.000	A=1.000
East Asian	Sub	84	C=0.00	A=1.00
Other Asian	Sub	24	C=0.00	A=1.00
Latin American 1	Sub	146	C=0.123	A=0.877
Latin American 2	Sub	610	C=0.011	A=0.989
South Asian	Sub	94	C=0.00	A=1.00
Other	Sub	470	C=0.098	A=0.902

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
gnomAD - Genomes	Global	Study-wide	75034	C=0.12857	A=0.87143
gnomAD - Genomes	European	Sub	34618	C=0.00540	A=0.99460
gnomAD - Genomes	African	Sub	28728	C=0.30782	A=0.69218
gnomAD - Genomes	American	Sub	6274	C=0.0768	A=0.9232
gnomAD - Genomes	East Asian	Sub	2910	C=0.0000	A=1.0000
gnomAD - Genomes	Ashkenazi Jewish	Sub	1424	C=0.0112	A=0.9888
gnomAD - Genomes	Other	Sub	1080	C=0.1102	A=0.8898
14KJPN	JAPANESE	Study-wide	27826	C=0.00014	A=0.99986
8.3KJPN	JAPANESE	Study-wide	16528	C=0.00030	A=0.99970
Allele Frequency Aggregator	Total	Global	11862	C=0.07073	A=0.92927
Allele Frequency Aggregator	European	Sub	7618	C=0.0046	A=0.9954
Allele Frequency Aggregator	African	Sub	2816	C=0.2603	A=0.7397
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.011	A=0.989
Allele Frequency Aggregator	Other	Sub	470	C=0.098	A=0.902
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.123	A=0.877
Allele Frequency Aggregator	Asian	Sub	108	C=0.000	A=1.000
Allele Frequency Aggregator	South Asian	Sub	94	C=0.00	A=1.00
1000Genomes_30x	Global	Study-wide	6404	C=0.0938	A=0.9062
1000Genomes_30x	African	Sub	1786	C=0.2940	A=0.7060
1000Genomes_30x	Europe	Sub	1266	C=0.0095	A=0.9905
1000Genomes_30x	South Asian	Sub	1202	C=0.0150	A=0.9850
1000Genomes_30x	East Asian	Sub	1170	C=0.0017	A=0.9983
1000Genomes_30x	American	Sub	980	C=0.045	A=0.955
1000Genomes	Global	Study-wide	5008	C=0.0767	A=0.9233
1000Genomes	African	Sub	1322	C=0.2572	A=0.7428
1000Genomes	East Asian	Sub	1008	C=0.0000	A=1.0000
1000Genomes	Europe	Sub	1006	C=0.0050	A=0.9950
1000Genomes	South Asian	Sub	978	C=0.014	A=0.986
1000Genomes	American	Sub	694	C=0.036	A=0.964
KOREAN population from KRGDB	KOREAN	Study-wide	2874	C=0.0010	A=0.9990, G=0.0000, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1808	C=0.0022	A=0.9978
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.002	A=0.998
SGDP_PRJ	Global	Study-wide	474	C=0.036	A=0.964
Qatari	Global	Study-wide	172	C=0.105	A=0.895
The Danish reference pan genome	Danish	Study-wide	38	C=0.00	A=1.00

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 1	NC_000001.11:g.55164C>A
GRCh38.p14 chr 1	NC_000001.11:g.55164C>G
GRCh38.p14 chr 1	NC_000001.11:g.55164C>T
GRCh37.p13 chr 1	NC_000001.10:g.55164C>A
GRCh37.p13 chr 1	NC_000001.10:g.55164C>G
GRCh37.p13 chr 1	NC_000001.10:g.55164C>T

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	C=	A	G	T
GRCh38.p14 chr 1	NC_000001.11:g.55164=	NC_000001.11:g.55164C>A	NC_000001.11:g.55164C>G	NC_000001.11:g.55164C>T
GRCh37.p13 chr 1	NC_000001.10:g.55164=	NC_000001.10:g.55164C>A	NC_000001.10:g.55164C>G	NC_000001.10:g.55164C>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#.

36 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss4348806	Mar 26, 2002 (103)
2	SC_JCM	ss4373667	Mar 26, 2002 (103)
3	BCM_SSAHASNP	ss14687330	Dec 05, 2003 (119)
4	CSHL-HAPMAP	ss16401900	Feb 27, 2004 (120)
5	BCMHGSC_JDW	ss87153195	Mar 25, 2008 (129)
6	ILLUMINA-UK	ss118438117	Feb 14, 2009 (130)
7	1000GENOMES	ss218190318	Jul 14, 2010 (132)
8	GMI	ss275679901	May 04, 2012 (137)
9	GMI	ss283987244	Apr 25, 2013 (138)
10	SSMP	ss647514820	Apr 25, 2013 (138)
11	EVA-GONL	ss974768742	Aug 21, 2014 (142)
12	1000GENOMES	ss1289335637	Aug 21, 2014 (142)
13	DDI	ss1425684543	Apr 01, 2015 (144)
14	EVA_GENOME_DK	ss1573850711	Apr 01, 2015 (144)
15	HAMMER_LAB	ss1793705020	Sep 08, 2015 (146)
16	WEILL_CORNELL_DGM	ss1917958222	Feb 12, 2016 (147)
17	GENOMED	ss1966667265	Jul 19, 2016 (147)
18	JJLAB	ss2019497521	Sep 14, 2016 (149)
19	SYSTEMSBIOZJU	ss2624264578	Nov 08, 2017 (151)
20	GRF	ss2697372976	Nov 08, 2017 (151)
21	GNOMAD	ss2750603652	Nov 08, 2017 (151)
22	SWEGEN	ss2986141905	Nov 08, 2017 (151)
23	CSHL	ss3343271533	Nov 08, 2017 (151)
24	EVA	ss3745720523	Jul 12, 2019 (153)
25	KHV_HUMAN_GENOMES	ss3798742453	Jul 12, 2019 (153)
26	EVA	ss3825981324	Apr 25, 2020 (154)
27	SGDP_PRJ	ss3847983918	Apr 25, 2020 (154)
28	KRGDB	ss3892823766	Apr 25, 2020 (154)
29	KOGIC	ss3943622537	Apr 25, 2020 (154)
30	TOMMO_GENOMICS	ss5142032626	Apr 25, 2021 (155)
31	1000G_HIGH_COVERAGE	ss5512474904	Oct 12, 2022 (156)
32	SANFORD_IMAGENETICS	ss5624742457	Oct 12, 2022 (156)
33	TOMMO_GENOMICS	ss5666165122	Oct 12, 2022 (156)
34	YY_MCH	ss5800240467	Oct 12, 2022 (156)
35	EVA	ss5831416611	Oct 12, 2022 (156)
36	EVA	ss5936581776	Oct 12, 2022 (156)
37	1000Genomes	NC_000001.10 - 55164	Oct 11, 2018 (152)
38	1000Genomes_30x	NC_000001.11 - 55164	Oct 12, 2022 (156)
39	The Danish reference pan genome	NC_000001.10 - 55164	Apr 25, 2020 (154)
40	gnomAD - Genomes	NC_000001.11 - 55164	Apr 25, 2021 (155)
41	Genome of the Netherlands Release 5	NC_000001.10 - 55164	Apr 25, 2020 (154)
42	KOREAN population from KRGDB	NC_000001.10 - 55164	Apr 25, 2020 (154)
43	Korean Genome Project	NC_000001.11 - 55164	Apr 25, 2020 (154)
44	Qatari	NC_000001.10 - 55164	Apr 25, 2020 (154)
45	SGDP_PRJ	NC_000001.10 - 55164	Apr 25, 2020 (154)
46	8.3KJPN	NC_000001.10 - 55164	Apr 25, 2021 (155)
47	14KJPN	NC_000001.11 - 55164	Oct 12, 2022 (156)
48	ALFA	NC_000001.11 - 55164	Apr 25, 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
ss87153195, ss118438117, ss275679901, ss283987244	NC_000001.9:45026:C:A	NC_000001.11:55163:C:A	(self)
212, 1357945, 8, 1160, 152, 898, 1933, ss218190318, ss647514820, ss974768742, ss1289335637, ss1425684543, ss1573850711, ss1793705020, ss1917958222, ss1966667265, ss2019497521, ss2624264578, ss2697372976, ss2750603652, ss2986141905, ss3343271533, ss3745720523, ss3825981324, ss3847983918, ss3892823766, ss5142032626, ss5624742457, ss5831416611, ss5936581776	NC_000001.10:55163:C:A	NC_000001.11:55163:C:A	(self)
839, 3918, 538, 2226, 4977521255, ss3798742453, ss3943622537, ss5512474904, ss5666165122, ss5800240467	NC_000001.11:55163:C:A	NC_000001.11:55163:C:A	(self)
ss14687330, ss16401900	NT_077402.1:45026:C:A	NC_000001.11:55163:C:A	(self)
ss4348806, ss4373667	NT_077402.2:45163:C:A	NC_000001.11:55163:C:A	(self)
1160, ss3892823766	NC_000001.10:55163:C:G	NC_000001.11:55163:C:G	(self)
1160, ss3892823766	NC_000001.10:55163:C:T	NC_000001.11:55163:C: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 rs3091274

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

rs3091274