Name: rs4615139
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.

rs4615139

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:169627374 (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: G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.022819 (6040/264690, TOPMED)
G=0.021493 (3014/140230, GnomAD)
G=0.00000 (0/28258, 14KJPN) (+ 15 more)
G=0.01725 (372/21564, ALFA)
G=0.00000 (0/16760, 8.3KJPN)
G=0.0255 (163/6404, 1000G_30x)
G=0.0232 (116/5008, 1000G)
G=0.0000 (0/3854, ALSPAC)
G=0.0003 (1/3708, TWINSUK)
G=0.0000 (0/2930, KOREAN)
C=0.0000 (0/2930, KOREAN)
G=0.0000 (0/1832, Korea1K)
G=0.000 (0/600, NorthernSweden)
G=0.009 (5/558, SGDP_PRJ)
G=0.028 (6/216, Qatari)
G=0.000 (0/214, Vietnamese)
G=0.00 (0/56, Siberian)
G=0.00 (0/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CLCN3 : 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	21564	G=0.01725	T=0.98275
European	Sub	14286	G=0.00063	T=0.99937
African	Sub	5568	G=0.0623	T=0.9377
African Others	Sub	198	G=0.086	T=0.914
African American	Sub	5370	G=0.0615	T=0.9385
Asian	Sub	112	G=0.000	T=1.000
East Asian	Sub	86	G=0.00	T=1.00
Other Asian	Sub	26	G=0.00	T=1.00
Latin American 1	Sub	146	G=0.014	T=0.986
Latin American 2	Sub	610	G=0.003	T=0.997
South Asian	Sub	98	G=0.00	T=1.00
Other	Sub	744	G=0.016	T=0.984

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	G=0.022819	T=0.977181
gnomAD - Genomes	Global	Study-wide	140230	G=0.021493	T=0.978507
gnomAD - Genomes	European	Sub	75964	G=0.00055	T=0.99945
gnomAD - Genomes	African	Sub	42012	G=0.06596	T=0.93404
gnomAD - Genomes	American	Sub	13648	G=0.01216	T=0.98784
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.0000	T=1.0000
gnomAD - Genomes	East Asian	Sub	3134	G=0.0000	T=1.0000
gnomAD - Genomes	Other	Sub	2148	G=0.0163	T=0.9837
14KJPN	JAPANESE	Study-wide	28258	G=0.00000	T=1.00000
Allele Frequency Aggregator	Total	Global	21564	G=0.01725	T=0.98275
Allele Frequency Aggregator	European	Sub	14286	G=0.00063	T=0.99937
Allele Frequency Aggregator	African	Sub	5568	G=0.0623	T=0.9377
Allele Frequency Aggregator	Other	Sub	744	G=0.016	T=0.984
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.003	T=0.997
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.014	T=0.986
Allele Frequency Aggregator	Asian	Sub	112	G=0.000	T=1.000
Allele Frequency Aggregator	South Asian	Sub	98	G=0.00	T=1.00
8.3KJPN	JAPANESE	Study-wide	16760	G=0.00000	T=1.00000
1000Genomes_30x	Global	Study-wide	6404	G=0.0255	T=0.9745
1000Genomes_30x	African	Sub	1786	G=0.0851	T=0.9149
1000Genomes_30x	Europe	Sub	1266	G=0.0032	T=0.9968
1000Genomes_30x	South Asian	Sub	1202	G=0.0000	T=1.0000
1000Genomes_30x	East Asian	Sub	1170	G=0.0000	T=1.0000
1000Genomes_30x	American	Sub	980	G=0.007	T=0.993
1000Genomes	Global	Study-wide	5008	G=0.0232	T=0.9768
1000Genomes	African	Sub	1322	G=0.0817	T=0.9183
1000Genomes	East Asian	Sub	1008	G=0.0000	T=1.0000
1000Genomes	Europe	Sub	1006	G=0.0020	T=0.9980
1000Genomes	South Asian	Sub	978	G=0.000	T=1.000
1000Genomes	American	Sub	694	G=0.009	T=0.991
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.0000	T=1.0000
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.0003	T=0.9997
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.0000	C=0.0000, T=1.0000
Korean Genome Project	KOREAN	Study-wide	1832	G=0.0000	T=1.0000
Northern Sweden	ACPOP	Study-wide	600	G=0.000	T=1.000
SGDP_PRJ	Global	Study-wide	558	G=0.009	T=0.991
Qatari	Global	Study-wide	216	G=0.028	T=0.972
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.000	T=1.000
Siberian	Global	Study-wide	56	G=0.00	T=1.00
The Danish reference pan genome	Danish	Study-wide	40	G=0.00	T=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 4	NC_000004.12:g.169627374G>C
GRCh38.p14 chr 4	NC_000004.12:g.169627374G>T
GRCh37.p13 chr 4	NC_000004.11:g.170548525G>C
GRCh37.p13 chr 4	NC_000004.11:g.170548525G>T
CLCN3 RefSeqGene	NG_029731.1:g.11854G>C
CLCN3 RefSeqGene	NG_029731.1:g.11854G>T

Gene: CLCN3, chloride voltage-gated channel 3 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CLCN3 transcript variant a	NM_001243372.2:c.-17+6311… NM_001243372.2:c.-17+6311G>C	N/A	Intron Variant
CLCN3 transcript variant b	NM_001829.4:c.-17+6311G>C	N/A	Intron Variant
CLCN3 transcript variant e	NM_173872.4:c.-17+6311G>C	N/A	Intron Variant
CLCN3 transcript variant c	NM_001243374.2:c.	N/A	Genic Upstream Transcript Variant
CLCN3 transcript variant X1	XM_005262726.4:c.	N/A	Genic Upstream Transcript Variant
CLCN3 transcript variant X2	XM_011531586.3:c.	N/A	Genic Upstream Transcript Variant
CLCN3 transcript variant X3	XM_047449584.1:c.	N/A	Genic Upstream Transcript Variant
CLCN3 transcript variant X4	XM_047449585.1:c.	N/A	Genic Upstream Transcript Variant
CLCN3 transcript variant X5	XM_047449586.1:c.	N/A	Genic 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	G=	C	T
GRCh38.p14 chr 4	NC_000004.12:g.169627374=	NC_000004.12:g.169627374G>C	NC_000004.12:g.169627374G>T
GRCh37.p13 chr 4	NC_000004.11:g.170548525=	NC_000004.11:g.170548525G>C	NC_000004.11:g.170548525G>T
CLCN3 RefSeqGene	NG_029731.1:g.11854=	NG_029731.1:g.11854G>C	NG_029731.1:g.11854G>T
CLCN3 transcript variant a	NM_001243372.1:c.-17+6311=	NM_001243372.1:c.-17+6311G>C	NM_001243372.1:c.-17+6311G>T
CLCN3 transcript variant a	NM_001243372.2:c.-17+6311=	NM_001243372.2:c.-17+6311G>C	NM_001243372.2:c.-17+6311G>T
CLCN3 transcript variant b	NM_001829.3:c.-17+6311=	NM_001829.3:c.-17+6311G>C	NM_001829.3:c.-17+6311G>T
CLCN3 transcript variant b	NM_001829.4:c.-17+6311=	NM_001829.4:c.-17+6311G>C	NM_001829.4:c.-17+6311G>T
CLCN3 transcript variant e	NM_173872.3:c.-17+6311=	NM_173872.3:c.-17+6311G>C	NM_173872.3:c.-17+6311G>T
CLCN3 transcript variant e	NM_173872.4:c.-17+6311=	NM_173872.4:c.-17+6311G>C	NM_173872.4:c.-17+6311G>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#.

74 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss6258550	Feb 20, 2003 (111)
2	BCM_SSAHASNP	ss10152248	Jul 11, 2003 (116)
3	CSHL-HAPMAP	ss20210041	Feb 27, 2004 (120)
4	SSAHASNP	ss22062070	Apr 05, 2004 (121)
5	PERLEGEN	ss23744152	Sep 20, 2004 (123)
6	HGSV	ss81008131	Dec 16, 2007 (130)
7	HGSV	ss86146894	Dec 16, 2007 (130)
8	BCMHGSC_JDW	ss92879743	Mar 24, 2008 (129)
9	HUMANGENOME_JCVI	ss98886552	Feb 06, 2009 (130)
10	BGI	ss105885100	Feb 06, 2009 (130)
11	1000GENOMES	ss108572062	Jan 23, 2009 (130)
12	1000GENOMES	ss111000817	Jan 25, 2009 (130)
13	ILLUMINA-UK	ss117289454	Feb 14, 2009 (130)
14	ENSEMBL	ss135047054	Dec 01, 2009 (131)
15	ENSEMBL	ss142523635	Dec 01, 2009 (131)
16	GMI	ss154597995	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss162781113	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss165051094	Jul 04, 2010 (132)
19	COMPLETE_GENOMICS	ss167415053	Jul 04, 2010 (132)
20	BUSHMAN	ss199518895	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss206259895	Jul 04, 2010 (132)
22	1000GENOMES	ss221364861	Jul 14, 2010 (132)
23	BL	ss253729304	May 09, 2011 (134)
24	GMI	ss278046796	May 04, 2012 (137)
25	GMI	ss285059440	Apr 25, 2013 (138)
26	PJP	ss293252622	May 09, 2011 (134)
27	TISHKOFF	ss558030656	Apr 25, 2013 (138)
28	SSMP	ss651860931	Apr 25, 2013 (138)
29	JMKIDD_LAB	ss1072183792	Aug 21, 2014 (142)
30	1000GENOMES	ss1312933257	Aug 21, 2014 (142)
31	DDI	ss1430146265	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1580896764	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1611763126	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1654757159	Apr 01, 2015 (144)
35	HAMMER_LAB	ss1802594509	Sep 08, 2015 (146)
36	WEILL_CORNELL_DGM	ss1924219831	Feb 12, 2016 (147)
37	GENOMED	ss1969941853	Jul 19, 2016 (147)
38	JJLAB	ss2022699863	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2150832990	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2269446611	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2625844252	Nov 08, 2017 (151)
42	GRF	ss2706338032	Nov 08, 2017 (151)
43	GNOMAD	ss2818457941	Nov 08, 2017 (151)
44	SWEGEN	ss2996010052	Nov 08, 2017 (151)
45	BIOINF_KMB_FNS_UNIBA	ss3025128436	Nov 08, 2017 (151)
46	CSHL	ss3346096309	Nov 08, 2017 (151)
47	URBANLAB	ss3647915667	Oct 12, 2018 (152)
48	EVA_DECODE	ss3713610517	Jul 13, 2019 (153)
49	ACPOP	ss3731855409	Jul 13, 2019 (153)
50	EVA	ss3762753445	Jul 13, 2019 (153)
51	PACBIO	ss3784942468	Jul 13, 2019 (153)
52	PACBIO	ss3790367297	Jul 13, 2019 (153)
53	PACBIO	ss3795242984	Jul 13, 2019 (153)
54	KHV_HUMAN_GENOMES	ss3805917234	Jul 13, 2019 (153)
55	EVA	ss3828954434	Apr 26, 2020 (154)
56	EVA	ss3837929900	Apr 26, 2020 (154)
57	EVA	ss3843371281	Apr 26, 2020 (154)
58	SGDP_PRJ	ss3860647540	Apr 26, 2020 (154)
59	KRGDB	ss3907018749	Apr 26, 2020 (154)
60	KOGIC	ss3955643848	Apr 26, 2020 (154)
61	TOPMED	ss4641735823	Apr 26, 2021 (155)
62	TOMMO_GENOMICS	ss5169270707	Apr 26, 2021 (155)
63	1000G_HIGH_COVERAGE	ss5262005297	Oct 17, 2022 (156)
64	EVA	ss5354082142	Oct 17, 2022 (156)
65	HUGCELL_USP	ss5460454361	Oct 17, 2022 (156)
66	EVA	ss5507838357	Oct 17, 2022 (156)
67	1000G_HIGH_COVERAGE	ss5544626475	Oct 17, 2022 (156)
68	SANFORD_IMAGENETICS	ss5636667858	Oct 17, 2022 (156)
69	TOMMO_GENOMICS	ss5704611295	Oct 17, 2022 (156)
70	YY_MCH	ss5805786404	Oct 17, 2022 (156)
71	EVA	ss5845102499	Oct 17, 2022 (156)
72	EVA	ss5854565222	Oct 17, 2022 (156)
73	EVA	ss5866620990	Oct 17, 2022 (156)
74	EVA	ss5965079486	Oct 17, 2022 (156)
75	1000Genomes	NC_000004.11 - 170548525	Oct 12, 2018 (152)
76	1000Genomes_30x	NC_000004.12 - 169627374	Oct 17, 2022 (156)
77	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 170548525	Oct 12, 2018 (152)
78	The Danish reference pan genome	NC_000004.11 - 170548525	Apr 26, 2020 (154)
79	gnomAD - Genomes	NC_000004.12 - 169627374	Apr 26, 2021 (155)
80	KOREAN population from KRGDB	NC_000004.11 - 170548525	Apr 26, 2020 (154)
81	Korean Genome Project	NC_000004.12 - 169627374	Apr 26, 2020 (154)
82	Northern Sweden	NC_000004.11 - 170548525	Jul 13, 2019 (153)
83	Qatari	NC_000004.11 - 170548525	Apr 26, 2020 (154)
84	SGDP_PRJ	NC_000004.11 - 170548525	Apr 26, 2020 (154)
85	Siberian	NC_000004.11 - 170548525	Apr 26, 2020 (154)
86	8.3KJPN	NC_000004.11 - 170548525	Apr 26, 2021 (155)
87	14KJPN	NC_000004.12 - 169627374	Oct 17, 2022 (156)
88	TopMed	NC_000004.12 - 169627374	Apr 26, 2021 (155)
89	UK 10K study - Twins	NC_000004.11 - 170548525	Oct 12, 2018 (152)
90	A Vietnamese Genetic Variation Database	NC_000004.11 - 170548525	Jul 13, 2019 (153)
91	ALFA	NC_000004.12 - 169627374	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).

Associated ID	History Updated (Build)
rs61613073	May 27, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
14196143, ss3907018749	NC_000004.11:170548524:G:C	NC_000004.12:169627373:G:C	(self)
ss81008131, ss86146894	NC_000004.9:170923254:G:T	NC_000004.12:169627373:G:T	(self)
ss92879743, ss108572062, ss111000817, ss117289454, ss162781113, ss165051094, ss167415053, ss199518895, ss206259895, ss253729304, ss278046796, ss285059440, ss293252622	NC_000004.10:170785099:G:T	NC_000004.12:169627373:G:T	(self)
24451670, 13602073, 7061703, 14196143, 5140274, 6261761, 12664520, 3349344, 27240014, 13602073, 3006957, ss221364861, ss558030656, ss651860931, ss1072183792, ss1312933257, ss1430146265, ss1580896764, ss1611763126, ss1654757159, ss1802594509, ss1924219831, ss1969941853, ss2022699863, ss2150832990, ss2625844252, ss2706338032, ss2818457941, ss2996010052, ss3346096309, ss3731855409, ss3762753445, ss3784942468, ss3790367297, ss3795242984, ss3828954434, ss3837929900, ss3860647540, ss3907018749, ss5169270707, ss5354082142, ss5507838357, ss5636667858, ss5845102499, ss5965079486	NC_000004.11:170548524:G:T	NC_000004.12:169627373:G:T	(self)
32152410, 173144746, 12021849, 38448399, 479113379, 6262028645, ss2269446611, ss3025128436, ss3647915667, ss3713610517, ss3805917234, ss3843371281, ss3955643848, ss4641735823, ss5262005297, ss5460454361, ss5544626475, ss5704611295, ss5805786404, ss5854565222, ss5866620990	NC_000004.12:169627373:G:T	NC_000004.12:169627373:G:T	(self)
ss6258550, ss23744152, ss98886552, ss105885100, ss135047054, ss142523635, ss154597995	NT_016354.19:95096245:G:T	NC_000004.12:169627373:G:T	(self)
ss10152248	NT_022792.15:2960045:G:T	NC_000004.12:169627373:G:T	(self)
ss20210041, ss22062070	NT_022792.16:2960045:G:T	NC_000004.12:169627373:G: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 rs4615139

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

rs4615139