Name: rs4330912
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.

rs4330912

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:155999637 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.467868 (123840/264690, TOPMED)
C=0.474885 (55552/116980, GnomAD)
G=0.14674 (4057/27648, 14KJPN) (+ 14 more)
G=0.14370 (2375/16528, 8.3KJPN)
G=0.4007 (3053/7620, ALFA)
G=0.3723 (2384/6404, 1000G_30x)
G=0.3752 (1879/5008, 1000G)
C=0.3656 (1409/3854, ALSPAC)
C=0.3711 (1376/3708, TWINSUK)
G=0.1099 (321/2920, KOREAN)
G=0.0929 (168/1808, Korea1K)
C=0.343 (342/998, GoNL)
C=0.369 (216/586, NorthernSweden)
C=0.303 (100/330, SGDP_PRJ)
C=0.481 (104/216, Qatari)
C=0.30 (12/40, GENOME_DK)
C=0.45 (10/22, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ARHGEF2-AS1 : 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	7620	C=0.5993	G=0.4007, T=0.0000
European	Sub	5426	C=0.4381	G=0.5619, T=0.0000
African	Sub	1710	C=1.0000	G=0.0000, T=0.0000
African Others	Sub	90	C=1.00	G=0.00, T=0.00
African American	Sub	1620	C=1.0000	G=0.0000, T=0.0000
Asian	Sub	94	C=1.00	G=0.00, T=0.00
East Asian	Sub	72	C=1.00	G=0.00, T=0.00
Other Asian	Sub	22	C=1.00	G=0.00, T=0.00
Latin American 1	Sub	28	C=1.00	G=0.00, T=0.00
Latin American 2	Sub	182	C=1.000	G=0.000, T=0.000
South Asian	Sub	18	C=1.00	G=0.00, T=0.00
Other	Sub	162	C=0.975	G=0.025, T=0.000

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	C=0.532132	G=0.467868
gnomAD - Genomes	Global	Study-wide	116980	C=0.474885	G=0.525115
gnomAD - Genomes	European	Sub	67894	C=0.35597	G=0.64403
gnomAD - Genomes	African	Sub	31014	C=0.73177	G=0.26823
gnomAD - Genomes	American	Sub	10300	C=0.39718	G=0.60282
gnomAD - Genomes	Ashkenazi Jewish	Sub	3204	C=0.4220	G=0.5780
gnomAD - Genomes	East Asian	Sub	2832	C=0.8665	G=0.1335
gnomAD - Genomes	Other	Sub	1736	C=0.4562	G=0.5438
14KJPN	JAPANESE	Study-wide	27648	C=0.85326	G=0.14674
8.3KJPN	JAPANESE	Study-wide	16528	C=0.85630	G=0.14370
Allele Frequency Aggregator	Total	Global	7620	C=0.5993	G=0.4007, T=0.0000
Allele Frequency Aggregator	European	Sub	5426	C=0.4381	G=0.5619, T=0.0000
Allele Frequency Aggregator	African	Sub	1710	C=1.0000	G=0.0000, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	182	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Other	Sub	162	C=0.975	G=0.025, T=0.000
Allele Frequency Aggregator	Asian	Sub	94	C=1.00	G=0.00, T=0.00
Allele Frequency Aggregator	Latin American 1	Sub	28	C=1.00	G=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	18	C=1.00	G=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.6277	G=0.3723
1000Genomes_30x	African	Sub	1786	C=0.8561	G=0.1439
1000Genomes_30x	Europe	Sub	1266	C=0.3878	G=0.6122
1000Genomes_30x	South Asian	Sub	1202	C=0.4434	G=0.5566
1000Genomes_30x	East Asian	Sub	1170	C=0.8709	G=0.1291
1000Genomes_30x	American	Sub	980	C=0.457	G=0.543
1000Genomes	Global	Study-wide	5008	C=0.6248	G=0.3752
1000Genomes	African	Sub	1322	C=0.8464	G=0.1536
1000Genomes	East Asian	Sub	1008	C=0.8661	G=0.1339
1000Genomes	Europe	Sub	1006	C=0.3847	G=0.6153
1000Genomes	South Asian	Sub	978	C=0.441	G=0.559
1000Genomes	American	Sub	694	C=0.460	G=0.540
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.3656	G=0.6344
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.3711	G=0.6289
KOREAN population from KRGDB	KOREAN	Study-wide	2920	C=0.8901	G=0.1099
Korean Genome Project	KOREAN	Study-wide	1808	C=0.9071	G=0.0929
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.343	G=0.657
Northern Sweden	ACPOP	Study-wide	586	C=0.369	G=0.631
SGDP_PRJ	Global	Study-wide	330	C=0.303	G=0.697
Qatari	Global	Study-wide	216	C=0.481	G=0.519
The Danish reference pan genome	Danish	Study-wide	40	C=0.30	G=0.70
Siberian	Global	Study-wide	22	C=0.45	G=0.55

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.155999637C>G
GRCh38.p14 chr 1	NC_000001.11:g.155999637C>T
GRCh37.p13 chr 1	NC_000001.10:g.155969428C>G
GRCh37.p13 chr 1	NC_000001.10:g.155969428C>T

Gene: ARHGEF2-AS1, uncharacterized ARHGEF2-AS1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ARHGEF2-AS1 transcript	XR_001738248.2:n.	N/A	Intron 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	C=	G	T
GRCh38.p14 chr 1	NC_000001.11:g.155999637=	NC_000001.11:g.155999637C>G	NC_000001.11:g.155999637C>T
GRCh37.p13 chr 1	NC_000001.10:g.155969428=	NC_000001.10:g.155969428C>G	NC_000001.10:g.155969428C>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#.

55 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss5753406	Feb 20, 2003 (111)
2	WI_SSAHASNP	ss11378258	Jul 11, 2003 (116)
3	HUMANGENOME_JCVI	ss99251698	Feb 04, 2009 (130)
4	ENSEMBL	ss138084569	Dec 01, 2009 (131)
5	ENSEMBL	ss142849149	Dec 01, 2009 (131)
6	COMPLETE_GENOMICS	ss167140706	Jul 04, 2010 (132)
7	BCM-HGSC-SUB	ss205540038	Jul 04, 2010 (132)
8	BL	ss253514157	May 09, 2011 (134)
9	GMI	ss276053629	May 04, 2012 (137)
10	GMI	ss284153797	Apr 25, 2013 (138)
11	PJP	ss290638397	May 09, 2011 (134)
12	1000GENOMES	ss328955843	May 09, 2011 (134)
13	SSMP	ss648418822	Apr 25, 2013 (138)
14	EVA-GONL	ss975690807	Aug 21, 2014 (142)
15	JMKIDD_LAB	ss1068274373	Aug 21, 2014 (142)
16	1000GENOMES	ss1292960681	Aug 21, 2014 (142)
17	DDI	ss1425980488	Apr 01, 2015 (144)
18	EVA_GENOME_DK	ss1574396049	Apr 01, 2015 (144)
19	EVA_DECODE	ss1585072552	Apr 01, 2015 (144)
20	EVA_UK10K_ALSPAC	ss1601231643	Apr 01, 2015 (144)
21	EVA_UK10K_TWINSUK	ss1644225676	Apr 01, 2015 (144)
22	WEILL_CORNELL_DGM	ss1918924344	Feb 12, 2016 (147)
23	USC_VALOUEV	ss2148002680	Dec 20, 2016 (150)
24	SYSTEMSBIOZJU	ss2624496545	Nov 08, 2017 (151)
25	GRF	ss2697975372	Nov 08, 2017 (151)
26	SWEGEN	ss2987766967	Nov 08, 2017 (151)
27	BIOINF_KMB_FNS_UNIBA	ss3023745543	Nov 08, 2017 (151)
28	CSHL	ss3343713690	Nov 08, 2017 (151)
29	URBANLAB	ss3646792908	Oct 11, 2018 (152)
30	EVA_DECODE	ss3687800119	Jul 12, 2019 (153)
31	ACPOP	ss3727492130	Jul 12, 2019 (153)
32	EVA	ss3746817932	Jul 12, 2019 (153)
33	PACBIO	ss3783568817	Jul 12, 2019 (153)
34	PACBIO	ss3789199724	Jul 12, 2019 (153)
35	PACBIO	ss3794071728	Jul 12, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3799818164	Jul 12, 2019 (153)
37	EVA	ss3826427735	Apr 25, 2020 (154)
38	EVA	ss3836608468	Apr 25, 2020 (154)
39	EVA	ss3842017744	Apr 25, 2020 (154)
40	SGDP_PRJ	ss3850023229	Apr 25, 2020 (154)
41	KRGDB	ss3895236964	Apr 25, 2020 (154)
42	KOGIC	ss3945671417	Apr 25, 2020 (154)
43	GNOMAD	ss4003909235	Apr 25, 2021 (155)
44	TOPMED	ss4468641019	Apr 25, 2021 (155)
45	TOMMO_GENOMICS	ss5146529756	Apr 25, 2021 (155)
46	1000G_HIGH_COVERAGE	ss5244324255	Oct 12, 2022 (156)
47	EVA	ss5322107717	Oct 12, 2022 (156)
48	1000G_HIGH_COVERAGE	ss5517668385	Oct 12, 2022 (156)
49	SANFORD_IMAGENETICS	ss5626607560	Oct 12, 2022 (156)
50	TOMMO_GENOMICS	ss5673741858	Oct 12, 2022 (156)
51	YY_MCH	ss5801266929	Oct 12, 2022 (156)
52	EVA	ss5832676755	Oct 12, 2022 (156)
53	EVA	ss5832676756	Oct 12, 2022 (156)
54	EVA	ss5910279594	Oct 12, 2022 (156)
55	EVA	ss5938401798	Oct 12, 2022 (156)
56	1000Genomes	NC_000001.10 - 155969428	Oct 11, 2018 (152)
57	1000Genomes_30x	NC_000001.11 - 155999637	Oct 12, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 155969428	Oct 11, 2018 (152)
59	The Danish reference pan genome	NC_000001.10 - 155969428	Apr 25, 2020 (154)
60	gnomAD - Genomes	NC_000001.11 - 155999637	Apr 25, 2021 (155)
61	Genome of the Netherlands Release 5	NC_000001.10 - 155969428	Apr 25, 2020 (154)
62	KOREAN population from KRGDB	NC_000001.10 - 155969428	Apr 25, 2020 (154)
63	Korean Genome Project	NC_000001.11 - 155999637	Apr 25, 2020 (154)
64	Northern Sweden	NC_000001.10 - 155969428	Jul 12, 2019 (153)
65	Qatari	NC_000001.10 - 155969428	Apr 25, 2020 (154)
66	SGDP_PRJ	NC_000001.10 - 155969428	Apr 25, 2020 (154)
67	Siberian	NC_000001.10 - 155969428	Apr 25, 2020 (154)
68	8.3KJPN	NC_000001.10 - 155969428	Apr 25, 2021 (155)
69	14KJPN	NC_000001.11 - 155999637	Oct 12, 2022 (156)
70	TopMed	NC_000001.11 - 155999637	Apr 25, 2021 (155)
71	UK 10K study - Twins	NC_000001.10 - 155969428	Oct 11, 2018 (152)
72	ALFA	NC_000001.11 - 155999637	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
ss167140706, ss205540038, ss253514157, ss276053629, ss284153797, ss290638397, ss1585072552	NC_000001.9:154236051:C:G	NC_000001.11:155999636:C:G	(self)
3753950, 2040837, 1711138, 885852, 2414358, 776995, 966274, 2040209, 519034, 4499063, 2040837, ss328955843, ss648418822, ss975690807, ss1068274373, ss1292960681, ss1425980488, ss1574396049, ss1601231643, ss1644225676, ss1918924344, ss2148002680, ss2624496545, ss2697975372, ss2987766967, ss3343713690, ss3727492130, ss3746817932, ss3783568817, ss3789199724, ss3794071728, ss3826427735, ss3836608468, ss3850023229, ss3895236964, ss5146529756, ss5322107717, ss5626607560, ss5832676755, ss5938401798	NC_000001.10:155969427:C:G	NC_000001.11:155999636:C:G	(self)
5194320, 27337567, 2049418, 7578962, 32247354, 3350853368, ss3023745543, ss3646792908, ss3687800119, ss3799818164, ss3842017744, ss3945671417, ss4003909235, ss4468641019, ss5244324255, ss5517668385, ss5673741858, ss5801266929, ss5910279594	NC_000001.11:155999636:C:G	NC_000001.11:155999636:C:G	(self)
ss5753406, ss99251698, ss138084569, ss142849149	NT_004487.19:7458069:C:G	NC_000001.11:155999636:C:G	(self)
ss11378258	NT_004668.15:2421828:C:G	NC_000001.11:155999636:C:G	(self)
ss5832676756	NC_000001.10:155969427:C:T	NC_000001.11:155999636:C:T
3350853368	NC_000001.11:155999636:C:T	NC_000001.11:155999636: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 rs4330912

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

rs4330912