Name: rs6833345
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.

rs6833345

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:105620009 (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 / T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.04101 (1159/28258, 14KJPN)
G=0.08113 (1660/20460, ALFA)
G=0.04183 (701/16760, 8.3KJPN) (+ 16 more)
G=0.1783 (1142/6404, 1000G_30x)
G=0.1745 (874/5008, 1000G)
G=0.1036 (464/4480, Estonian)
G=0.1305 (503/3854, ALSPAC)
G=0.1394 (517/3708, TWINSUK)
G=0.0392 (115/2930, KOREAN)
G=0.2439 (461/1890, HapMap)
G=0.0453 (83/1832, Korea1K)
G=0.153 (153/998, GoNL)
G=0.135 (81/600, NorthernSweden)
G=0.255 (55/216, Qatari)
G=0.028 (6/216, Vietnamese)
T=0.413 (52/126, SGDP_PRJ)
G=0.10 (4/40, GENOME_DK)
T=0.5 (5/10, Siberian)
G=0.5 (5/10, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ARHGEF38 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	20460	T=0.91887	A=0.00000, C=0.00000, G=0.08113	0.853763	0.016031	0.130205	32
European	Sub	16288	T=0.93111	A=0.00000, C=0.00000, G=0.06889	0.871439	0.009209	0.119352	21
African	Sub	2432	T=0.8187	A=0.0000, C=0.0000, G=0.1813	0.703125	0.065789	0.231086	32
African Others	Sub	86	T=0.86	A=0.00, C=0.00, G=0.14	0.72093	0.0	0.27907	1
African American	Sub	2346	T=0.8171	A=0.0000, C=0.0000, G=0.1829	0.702472	0.068201	0.229327	34
Asian	Sub	120	T=1.000	A=0.000, C=0.000, G=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	94	T=1.00	A=0.00, C=0.00, G=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	26	T=1.00	A=0.00, C=0.00, G=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	108	T=0.944	A=0.000, C=0.000, G=0.056	0.925926	0.037037	0.037037	13
Latin American 2	Sub	534	T=0.983	A=0.000, C=0.000, G=0.017	0.970037	0.003745	0.026217	7
South Asian	Sub	78	T=1.00	A=0.00, C=0.00, G=0.00	1.0	0.0	0.0	N/A
Other	Sub	900	T=0.909	A=0.000, C=0.000, G=0.091	0.831111	0.013333	0.155556	1

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
14KJPN	JAPANESE	Study-wide	28258	T=0.95899	G=0.04101
Allele Frequency Aggregator	Total	Global	20460	T=0.91887	A=0.00000, C=0.00000, G=0.08113
Allele Frequency Aggregator	European	Sub	16288	T=0.93111	A=0.00000, C=0.00000, G=0.06889
Allele Frequency Aggregator	African	Sub	2432	T=0.8187	A=0.0000, C=0.0000, G=0.1813
Allele Frequency Aggregator	Other	Sub	900	T=0.909	A=0.000, C=0.000, G=0.091
Allele Frequency Aggregator	Latin American 2	Sub	534	T=0.983	A=0.000, C=0.000, G=0.017
Allele Frequency Aggregator	Asian	Sub	120	T=1.000	A=0.000, C=0.000, G=0.000
Allele Frequency Aggregator	Latin American 1	Sub	108	T=0.944	A=0.000, C=0.000, G=0.056
Allele Frequency Aggregator	South Asian	Sub	78	T=1.00	A=0.00, C=0.00, G=0.00
8.3KJPN	JAPANESE	Study-wide	16760	T=0.95817	G=0.04183
1000Genomes_30x	Global	Study-wide	6404	T=0.8217	G=0.1783
1000Genomes_30x	African	Sub	1786	T=0.6254	G=0.3746
1000Genomes_30x	Europe	Sub	1266	T=0.8404	G=0.1596
1000Genomes_30x	South Asian	Sub	1202	T=0.9243	G=0.0757
1000Genomes_30x	East Asian	Sub	1170	T=0.9684	G=0.0316
1000Genomes_30x	American	Sub	980	T=0.854	G=0.146
1000Genomes	Global	Study-wide	5008	T=0.8255	G=0.1745
1000Genomes	African	Sub	1322	T=0.6218	G=0.3782
1000Genomes	East Asian	Sub	1008	T=0.9673	G=0.0327
1000Genomes	Europe	Sub	1006	T=0.8350	G=0.1650
1000Genomes	South Asian	Sub	978	T=0.925	G=0.075
1000Genomes	American	Sub	694	T=0.853	G=0.147
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.8964	G=0.1036
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.8695	G=0.1305
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.8606	G=0.1394
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.9608	G=0.0392
HapMap	Global	Study-wide	1890	T=0.7561	G=0.2439
HapMap	American	Sub	770	T=0.869	G=0.131
HapMap	African	Sub	692	T=0.552	G=0.448
HapMap	Asian	Sub	252	T=0.968	G=0.032
HapMap	Europe	Sub	176	T=0.761	G=0.239
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9547	G=0.0453
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.847	G=0.153
Northern Sweden	ACPOP	Study-wide	600	T=0.865	G=0.135
Qatari	Global	Study-wide	216	T=0.745	G=0.255
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.972	G=0.028
SGDP_PRJ	Global	Study-wide	126	T=0.413	G=0.587
The Danish reference pan genome	Danish	Study-wide	40	T=0.90	G=0.10
Siberian	Global	Study-wide	10	T=0.5	G=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 4	NC_000004.12:g.105620009T>A
GRCh38.p14 chr 4	NC_000004.12:g.105620009T>C
GRCh38.p14 chr 4	NC_000004.12:g.105620009T>G
GRCh37.p13 chr 4	NC_000004.11:g.106541166T>A
GRCh37.p13 chr 4	NC_000004.11:g.106541166T>C
GRCh37.p13 chr 4	NC_000004.11:g.106541166T>G

Gene: ARHGEF38, Rho guanine nucleotide exchange factor 38 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ARHGEF38 transcript variant 1	NM_001242729.2:c.508+6502… NM_001242729.2:c.508+6502T>A	N/A	Intron Variant
ARHGEF38 transcript variant 2	NM_017700.2:c.508+6502T>A	N/A	Intron Variant
ARHGEF38 transcript variant X5	XM_011532050.3:c.13+6502T… XM_011532050.3:c.13+6502T>A	N/A	Intron Variant
ARHGEF38 transcript variant X8	XM_011532051.3:c.508+6502… XM_011532051.3:c.508+6502T>A	N/A	Intron Variant
ARHGEF38 transcript variant X7	XM_006714244.4:c.	N/A	Genic Upstream Transcript Variant
ARHGEF38 transcript variant X2	XR_001741247.3:n.	N/A	Intron Variant
ARHGEF38 transcript variant X4	XR_007057934.1:n.	N/A	Intron Variant
ARHGEF38 transcript variant X3	XR_938749.4:n.	N/A	Intron Variant
ARHGEF38 transcript variant X1	XR_938750.4:n.	N/A	Intron Variant
ARHGEF38 transcript variant X6	XR_938751.4: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	T=	A	C	G
GRCh38.p14 chr 4	NC_000004.12:g.105620009=	NC_000004.12:g.105620009T>A	NC_000004.12:g.105620009T>C	NC_000004.12:g.105620009T>G
GRCh37.p13 chr 4	NC_000004.11:g.106541166=	NC_000004.11:g.106541166T>A	NC_000004.11:g.106541166T>C	NC_000004.11:g.106541166T>G
ARHGEF38 transcript variant 1	NM_001242729.1:c.508+6502=	NM_001242729.1:c.508+6502T>A	NM_001242729.1:c.508+6502T>C	NM_001242729.1:c.508+6502T>G
ARHGEF38 transcript variant 1	NM_001242729.2:c.508+6502=	NM_001242729.2:c.508+6502T>A	NM_001242729.2:c.508+6502T>C	NM_001242729.2:c.508+6502T>G
ARHGEF38 transcript variant 2	NM_017700.1:c.508+6502=	NM_017700.1:c.508+6502T>A	NM_017700.1:c.508+6502T>C	NM_017700.1:c.508+6502T>G
ARHGEF38 transcript variant 2	NM_017700.2:c.508+6502=	NM_017700.2:c.508+6502T>A	NM_017700.2:c.508+6502T>C	NM_017700.2:c.508+6502T>G
ARHGEF38 transcript variant X5	XM_011532050.3:c.13+6502=	XM_011532050.3:c.13+6502T>A	XM_011532050.3:c.13+6502T>C	XM_011532050.3:c.13+6502T>G
ARHGEF38 transcript variant X8	XM_011532051.3:c.508+6502=	XM_011532051.3:c.508+6502T>A	XM_011532051.3:c.508+6502T>C	XM_011532051.3:c.508+6502T>G

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#.

66 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss10142733	Jul 11, 2003 (116)
2	PERLEGEN	ss23279900	Sep 20, 2004 (123)
3	ILLUMINA	ss65812400	Oct 15, 2006 (127)
4	ILLUMINA	ss74899083	Dec 06, 2007 (129)
5	BGI	ss104102937	Dec 01, 2009 (131)
6	1000GENOMES	ss108201760	Jan 23, 2009 (130)
7	ILLUMINA-UK	ss117129462	Feb 14, 2009 (130)
8	KRIBB_YJKIM	ss119528287	Dec 01, 2009 (131)
9	COMPLETE_GENOMICS	ss166987733	Jul 04, 2010 (132)
10	ILLUMINA	ss174133641	Jul 04, 2010 (132)
11	BUSHMAN	ss198974071	Jul 04, 2010 (132)
12	1000GENOMES	ss211464782	Jul 14, 2010 (132)
13	1000GENOMES	ss221122282	Jul 14, 2010 (132)
14	1000GENOMES	ss232531460	Jul 14, 2010 (132)
15	1000GENOMES	ss239792203	Jul 15, 2010 (132)
16	BL	ss253400169	May 09, 2011 (134)
17	ILLUMINA	ss537399456	Sep 08, 2015 (146)
18	TISHKOFF	ss557748551	Apr 25, 2013 (138)
19	SSMP	ss651551037	Apr 25, 2013 (138)
20	EVA-GONL	ss980498524	Aug 21, 2014 (142)
21	JMKIDD_LAB	ss1071821082	Aug 21, 2014 (142)
22	1000GENOMES	ss1311152847	Aug 21, 2014 (142)
23	DDI	ss1429996416	Apr 01, 2015 (144)
24	EVA_GENOME_DK	ss1580704691	Apr 01, 2015 (144)
25	EVA_DECODE	ss1590002950	Apr 01, 2015 (144)
26	EVA_UK10K_ALSPAC	ss1610831110	Apr 01, 2015 (144)
27	EVA_UK10K_TWINSUK	ss1653825143	Apr 01, 2015 (144)
28	EVA_SVP	ss1712695949	Apr 01, 2015 (144)
29	HAMMER_LAB	ss1801967195	Sep 08, 2015 (146)
30	WEILL_CORNELL_DGM	ss1923736739	Feb 12, 2016 (147)
31	JJLAB	ss2022453191	Sep 14, 2016 (149)
32	USC_VALOUEV	ss2150582785	Dec 20, 2016 (150)
33	HUMAN_LONGEVITY	ss2265785553	Dec 20, 2016 (150)
34	ILLUMINA	ss2635135822	Nov 08, 2017 (151)
35	GRF	ss2706060534	Nov 08, 2017 (151)
36	GNOMAD	ss2813355322	Nov 08, 2017 (151)
37	SWEGEN	ss2995281646	Nov 08, 2017 (151)
38	BIOINF_KMB_FNS_UNIBA	ss3025002079	Nov 08, 2017 (151)
39	CSHL	ss3345881847	Nov 08, 2017 (151)
40	ILLUMINA	ss3629034144	Oct 12, 2018 (152)
41	ILLUMINA	ss3638503908	Oct 12, 2018 (152)
42	ILLUMINA	ss3643453913	Oct 12, 2018 (152)
43	EGCUT_WGS	ss3663180017	Jul 13, 2019 (153)
44	EVA_DECODE	ss3712741921	Jul 13, 2019 (153)
45	ACPOP	ss3731460275	Jul 13, 2019 (153)
46	EVA	ss3762216119	Jul 13, 2019 (153)
47	KHV_HUMAN_GENOMES	ss3805365771	Jul 13, 2019 (153)
48	EVA	ss3828724601	Apr 26, 2020 (154)
49	EVA	ss3837804232	Apr 26, 2020 (154)
50	EVA	ss3843242846	Apr 26, 2020 (154)
51	SGDP_PRJ	ss3859700231	Apr 26, 2020 (154)
52	KRGDB	ss3905983626	Apr 26, 2020 (154)
53	KOGIC	ss3954817602	Apr 26, 2020 (154)
54	TOPMED	ss4626187953	Apr 26, 2021 (155)
55	TOPMED	ss4626187954	Apr 26, 2021 (155)
56	TOMMO_GENOMICS	ss5167267891	Apr 26, 2021 (155)
57	1000G_HIGH_COVERAGE	ss5260438948	Oct 13, 2022 (156)
58	HUGCELL_USP	ss5459064369	Oct 13, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5542185803	Oct 13, 2022 (156)
60	SANFORD_IMAGENETICS	ss5635752651	Oct 13, 2022 (156)
61	TOMMO_GENOMICS	ss5702052859	Oct 13, 2022 (156)
62	YY_MCH	ss5805389649	Oct 13, 2022 (156)
63	EVA	ss5844482722	Oct 13, 2022 (156)
64	EVA	ss5854372918	Oct 13, 2022 (156)
65	EVA	ss5864849305	Oct 13, 2022 (156)
66	EVA	ss5964148602	Oct 13, 2022 (156)
67	1000Genomes	NC_000004.11 - 106541166	Oct 12, 2018 (152)
68	1000Genomes_30x	NC_000004.12 - 105620009	Oct 13, 2022 (156)
69	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 106541166	Oct 12, 2018 (152)
70	Genetic variation in the Estonian population	NC_000004.11 - 106541166	Oct 12, 2018 (152)
71	The Danish reference pan genome	NC_000004.11 - 106541166	Apr 26, 2020 (154)
72	gnomAD - Genomes Submission ignored due to conflicting rows: Row 160120203 (NC_000004.12:105620008:T:C 2/140052) Row 160120204 (NC_000004.12:105620008:T:G 29224/140012)	-	Apr 26, 2021 (155)
73	gnomAD - Genomes Submission ignored due to conflicting rows: Row 160120203 (NC_000004.12:105620008:T:C 2/140052) Row 160120204 (NC_000004.12:105620008:T:G 29224/140012)	-	Apr 26, 2021 (155)
74	Genome of the Netherlands Release 5	NC_000004.11 - 106541166	Apr 26, 2020 (154)
75	HapMap	NC_000004.12 - 105620009	Apr 26, 2020 (154)
76	KOREAN population from KRGDB	NC_000004.11 - 106541166	Apr 26, 2020 (154)
77	Korean Genome Project	NC_000004.12 - 105620009	Apr 26, 2020 (154)
78	Northern Sweden	NC_000004.11 - 106541166	Jul 13, 2019 (153)
79	Qatari	NC_000004.11 - 106541166	Apr 26, 2020 (154)
80	SGDP_PRJ	NC_000004.11 - 106541166	Apr 26, 2020 (154)
81	Siberian	NC_000004.11 - 106541166	Apr 26, 2020 (154)
82	8.3KJPN	NC_000004.11 - 106541166	Apr 26, 2021 (155)
83	14KJPN	NC_000004.12 - 105620009	Oct 13, 2022 (156)
84	TopMed Submission ignored due to conflicting rows: Row 463565509 (NC_000004.12:105620008:T:C 2/264690) Row 463565510 (NC_000004.12:105620008:T:G 56960/264690)	-	Apr 26, 2021 (155)
85	TopMed Submission ignored due to conflicting rows: Row 463565509 (NC_000004.12:105620008:T:C 2/264690) Row 463565510 (NC_000004.12:105620008:T:G 56960/264690)	-	Apr 26, 2021 (155)
86	UK 10K study - Twins	NC_000004.11 - 106541166	Oct 12, 2018 (152)
87	A Vietnamese Genetic Variation Database	NC_000004.11 - 106541166	Jul 13, 2019 (153)
88	ALFA	NC_000004.12 - 105620009	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
6460342808	NC_000004.12:105620008:T:A	NC_000004.12:105620008:T:A	(self)
ss2813355322	NC_000004.11:106541165:T:C	NC_000004.12:105620008:T:C	(self)
6460342808, ss2265785553, ss4626187953	NC_000004.12:105620008:T:C	NC_000004.12:105620008:T:C	(self)
ss108201760, ss117129462, ss166987733, ss198974071, ss211464782, ss253400169, ss1590002950, ss1712695949, ss2635135822, ss3643453913	NC_000004.10:106760614:T:G	NC_000004.12:105620008:T:G	(self)
22601668, 12576256, 8918265, 6869630, 5560973, 13161020, 4745140, 5778669, 11717211, 3099139, 25237198, 12576256, 2764798, ss221122282, ss232531460, ss239792203, ss537399456, ss557748551, ss651551037, ss980498524, ss1071821082, ss1311152847, ss1429996416, ss1580704691, ss1610831110, ss1653825143, ss1801967195, ss1923736739, ss2022453191, ss2150582785, ss2706060534, ss2813355322, ss2995281646, ss3345881847, ss3629034144, ss3638503908, ss3663180017, ss3731460275, ss3762216119, ss3828724601, ss3837804232, ss3859700231, ss3905983626, ss5167267891, ss5635752651, ss5844482722, ss5964148602	NC_000004.11:106541165:T:G	NC_000004.12:105620008:T:G	(self)
29711738, 2678049, 11195603, 35889963, 6460342808, ss2265785553, ss3025002079, ss3712741921, ss3805365771, ss3843242846, ss3954817602, ss4626187954, ss5260438948, ss5459064369, ss5542185803, ss5702052859, ss5805389649, ss5854372918, ss5864849305	NC_000004.12:105620008:T:G	NC_000004.12:105620008:T:G	(self)
ss10142733	NT_016354.15:31036295:T:G	NC_000004.12:105620008:T:G	(self)
ss23279900, ss65812400, ss74899083, ss104102937, ss119528287, ss174133641	NT_016354.19:31088886:T:G	NC_000004.12:105620008:T:G	(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 rs6833345

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs6833345