Name: rs10274425
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.

rs10274425

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:143319073 (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>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.375522 (99397/264690, TOPMED)
A=0.367722 (51473/139978, GnomAD)
A=0.01628 (460/28258, 14KJPN) (+ 19 more)
A=0.33532 (8609/25674, ALFA)
A=0.01575 (264/16758, 8.3KJPN)
A=0.3260 (2088/6404, 1000G_30x)
A=0.3203 (1604/5008, 1000G)
A=0.2551 (1143/4480, Estonian)
A=0.3121 (1203/3854, ALSPAC)
A=0.3293 (1221/3708, TWINSUK)
A=0.0322 (94/2922, KOREAN)
A=0.0382 (70/1832, Korea1K)
A=0.3393 (602/1774, HapMap)
A=0.300 (299/998, GoNL)
A=0.232 (145/626, Chileans)
A=0.262 (157/600, NorthernSweden)
G=0.444 (96/216, Qatari)
A=0.047 (10/214, Vietnamese)
G=0.344 (73/212, SGDP_PRJ)
A=0.38 (15/40, GENOME_DK)
G=0.50 (9/18, Siberian)
A=0.50 (9/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CLCN1 : 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	25674	G=0.66468	A=0.33532
European	Sub	17398	G=0.69451	A=0.30549
African	Sub	3624	G=0.4451	A=0.5549
African Others	Sub	126	G=0.365	A=0.635
African American	Sub	3498	G=0.4480	A=0.5520
Asian	Sub	160	G=0.963	A=0.037
East Asian	Sub	102	G=0.971	A=0.029
Other Asian	Sub	58	G=0.95	A=0.05
Latin American 1	Sub	290	G=0.579	A=0.421
Latin American 2	Sub	2750	G=0.7589	A=0.2411
South Asian	Sub	110	G=0.718	A=0.282
Other	Sub	1342	G=0.6565	A=0.3435

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.624478	A=0.375522
gnomAD - Genomes	Global	Study-wide	139978	G=0.632278	A=0.367722
gnomAD - Genomes	European	Sub	75820	G=0.70652	A=0.29348
gnomAD - Genomes	African	Sub	41922	G=0.44602	A=0.55398
gnomAD - Genomes	American	Sub	13640	G=0.71884	A=0.28116
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.6255	A=0.3745
gnomAD - Genomes	East Asian	Sub	3126	G=0.9495	A=0.0505
gnomAD - Genomes	Other	Sub	2148	G=0.6462	A=0.3538
14KJPN	JAPANESE	Study-wide	28258	G=0.98372	A=0.01628
Allele Frequency Aggregator	Total	Global	25674	G=0.66468	A=0.33532
Allele Frequency Aggregator	European	Sub	17398	G=0.69451	A=0.30549
Allele Frequency Aggregator	African	Sub	3624	G=0.4451	A=0.5549
Allele Frequency Aggregator	Latin American 2	Sub	2750	G=0.7589	A=0.2411
Allele Frequency Aggregator	Other	Sub	1342	G=0.6565	A=0.3435
Allele Frequency Aggregator	Latin American 1	Sub	290	G=0.579	A=0.421
Allele Frequency Aggregator	Asian	Sub	160	G=0.963	A=0.037
Allele Frequency Aggregator	South Asian	Sub	110	G=0.718	A=0.282
8.3KJPN	JAPANESE	Study-wide	16758	G=0.98425	A=0.01575
1000Genomes_30x	Global	Study-wide	6404	G=0.6740	A=0.3260
1000Genomes_30x	African	Sub	1786	G=0.3981	A=0.6019
1000Genomes_30x	Europe	Sub	1266	G=0.6998	A=0.3002
1000Genomes_30x	South Asian	Sub	1202	G=0.7105	A=0.2895
1000Genomes_30x	East Asian	Sub	1170	G=0.9590	A=0.0410
1000Genomes_30x	American	Sub	980	G=0.758	A=0.242
1000Genomes	Global	Study-wide	5008	G=0.6797	A=0.3203
1000Genomes	African	Sub	1322	G=0.3994	A=0.6006
1000Genomes	East Asian	Sub	1008	G=0.9603	A=0.0397
1000Genomes	Europe	Sub	1006	G=0.6909	A=0.3091
1000Genomes	South Asian	Sub	978	G=0.707	A=0.293
1000Genomes	American	Sub	694	G=0.752	A=0.248
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7449	A=0.2551
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.6879	A=0.3121
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.6707	A=0.3293
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9678	A=0.0322
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9618	A=0.0382
HapMap	Global	Study-wide	1774	G=0.6607	A=0.3393
HapMap	African	Sub	682	G=0.440	A=0.560
HapMap	American	Sub	664	G=0.774	A=0.226
HapMap	Asian	Sub	254	G=0.969	A=0.031
HapMap	Europe	Sub	174	G=0.644	A=0.356
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.700	A=0.300
Chileans	Chilean	Study-wide	626	G=0.768	A=0.232
Northern Sweden	ACPOP	Study-wide	600	G=0.738	A=0.262
Qatari	Global	Study-wide	216	G=0.444	A=0.556
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.953	A=0.047
SGDP_PRJ	Global	Study-wide	212	G=0.344	A=0.656
The Danish reference pan genome	Danish	Study-wide	40	G=0.62	A=0.38
Siberian	Global	Study-wide	18	G=0.50	A=0.50

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 7	NC_000007.14:g.143319073G>A
GRCh37.p13 chr 7	NC_000007.13:g.143016166G>A
CLCN1 RefSeqGene	NG_009815.2:g.7948G>A

Gene: CLCN1, chloride voltage-gated channel 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CLCN1 transcript variant 1	NM_000083.3:c.181-682G>A	N/A	Intron Variant
CLCN1 transcript variant 2	NR_046453.2: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	G=	A
GRCh38.p14 chr 7	NC_000007.14:g.143319073=	NC_000007.14:g.143319073G>A
GRCh37.p13 chr 7	NC_000007.13:g.143016166=	NC_000007.13:g.143016166G>A
CLCN1 RefSeqGene	NG_009815.2:g.7948=	NG_009815.2:g.7948G>A
CLCN1 transcript variant 1	NM_000083.2:c.181-682=	NM_000083.2:c.181-682G>A
CLCN1 transcript variant 1	NM_000083.3:c.181-682=	NM_000083.3:c.181-682G>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#.

59 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WUGSC_SSAHASNP	ss14144254	Dec 05, 2003 (119)
2	AFFY	ss66460997	Dec 01, 2006 (127)
3	AFFY	ss76259638	Dec 07, 2007 (129)
4	KRIBB_YJKIM	ss82713380	Dec 15, 2007 (130)
5	HGSV	ss85547893	Dec 14, 2007 (130)
6	1000GENOMES	ss114565977	Jan 25, 2009 (130)
7	ILLUMINA-UK	ss116355630	Feb 14, 2009 (130)
8	COMPLETE_GENOMICS	ss165578869	Jul 04, 2010 (132)
9	AFFY	ss173011244	Jul 04, 2010 (132)
10	BUSHMAN	ss198414957	Jul 04, 2010 (132)
11	BCM-HGSC-SUB	ss208298657	Jul 04, 2010 (132)
12	1000GENOMES	ss223382296	Jul 14, 2010 (132)
13	1000GENOMES	ss234203736	Jul 15, 2010 (132)
14	BL	ss254732104	May 09, 2011 (134)
15	GMI	ss279566743	May 04, 2012 (137)
16	TISHKOFF	ss560362899	Apr 25, 2013 (138)
17	SSMP	ss654776052	Apr 25, 2013 (138)
18	EVA-GONL	ss984900695	Aug 21, 2014 (142)
19	JMKIDD_LAB	ss1075056817	Aug 21, 2014 (142)
20	1000GENOMES	ss1327524749	Aug 21, 2014 (142)
21	DDI	ss1431308832	Apr 01, 2015 (144)
22	EVA_GENOME_DK	ss1582440331	Apr 01, 2015 (144)
23	EVA_DECODE	ss1594490221	Apr 01, 2015 (144)
24	EVA_UK10K_ALSPAC	ss1619424662	Apr 01, 2015 (144)
25	EVA_UK10K_TWINSUK	ss1662418695	Apr 01, 2015 (144)
26	EVA_SVP	ss1712994650	Apr 01, 2015 (144)
27	HAMMER_LAB	ss1805265904	Sep 08, 2015 (146)
28	WEILL_CORNELL_DGM	ss1928156759	Feb 12, 2016 (147)
29	GENOMED	ss1970838527	Jul 19, 2016 (147)
30	JJLAB	ss2024767982	Sep 14, 2016 (149)
31	USC_VALOUEV	ss2152993187	Dec 20, 2016 (150)
32	HUMAN_LONGEVITY	ss2298656148	Dec 20, 2016 (150)
33	GRF	ss2708716268	Nov 08, 2017 (151)
34	GNOMAD	ss2860223641	Nov 08, 2017 (151)
35	SWEGEN	ss3002202006	Nov 08, 2017 (151)
36	BIOINF_KMB_FNS_UNIBA	ss3026173538	Nov 08, 2017 (151)
37	CSHL	ss3347889724	Nov 08, 2017 (151)
38	EGCUT_WGS	ss3669949892	Jul 13, 2019 (153)
39	EVA_DECODE	ss3720886605	Jul 13, 2019 (153)
40	ACPOP	ss3735155637	Jul 13, 2019 (153)
41	EVA	ss3767280077	Jul 13, 2019 (153)
42	KHV_HUMAN_GENOMES	ss3810442355	Jul 13, 2019 (153)
43	EVA	ss3830869713	Apr 26, 2020 (154)
44	SGDP_PRJ	ss3868599107	Apr 26, 2020 (154)
45	KRGDB	ss3915983932	Apr 26, 2020 (154)
46	KOGIC	ss3962768178	Apr 26, 2020 (154)
47	TOPMED	ss4767160369	Apr 26, 2021 (155)
48	TOMMO_GENOMICS	ss5186028511	Apr 26, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5275088149	Oct 13, 2022 (156)
50	EVA	ss5377412118	Oct 13, 2022 (156)
51	HUGCELL_USP	ss5471934786	Oct 13, 2022 (156)
52	1000G_HIGH_COVERAGE	ss5564420798	Oct 13, 2022 (156)
53	SANFORD_IMAGENETICS	ss5644181200	Oct 13, 2022 (156)
54	TOMMO_GENOMICS	ss5727172286	Oct 13, 2022 (156)
55	YY_MCH	ss5809182848	Oct 13, 2022 (156)
56	EVA	ss5823658549	Oct 13, 2022 (156)
57	EVA	ss5856135746	Oct 13, 2022 (156)
58	EVA	ss5861281560	Oct 13, 2022 (156)
59	EVA	ss5973387847	Oct 13, 2022 (156)
60	1000Genomes	NC_000007.13 - 143016166	Oct 12, 2018 (152)
61	1000Genomes_30x	NC_000007.14 - 143319073	Oct 13, 2022 (156)
62	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 143016166	Oct 12, 2018 (152)
63	Chileans	NC_000007.13 - 143016166	Apr 26, 2020 (154)
64	Genetic variation in the Estonian population	NC_000007.13 - 143016166	Oct 12, 2018 (152)
65	The Danish reference pan genome	NC_000007.13 - 143016166	Apr 26, 2020 (154)
66	gnomAD - Genomes	NC_000007.14 - 143319073	Apr 26, 2021 (155)
67	Genome of the Netherlands Release 5	NC_000007.13 - 143016166	Apr 26, 2020 (154)
68	HapMap	NC_000007.14 - 143319073	Apr 26, 2020 (154)
69	KOREAN population from KRGDB	NC_000007.13 - 143016166	Apr 26, 2020 (154)
70	Korean Genome Project	NC_000007.14 - 143319073	Apr 26, 2020 (154)
71	Northern Sweden	NC_000007.13 - 143016166	Jul 13, 2019 (153)
72	Qatari	NC_000007.13 - 143016166	Apr 26, 2020 (154)
73	SGDP_PRJ	NC_000007.13 - 143016166	Apr 26, 2020 (154)
74	Siberian	NC_000007.13 - 143016166	Apr 26, 2020 (154)
75	8.3KJPN	NC_000007.13 - 143016166	Apr 26, 2021 (155)
76	14KJPN	NC_000007.14 - 143319073	Oct 13, 2022 (156)
77	TopMed	NC_000007.14 - 143319073	Apr 26, 2021 (155)
78	UK 10K study - Twins	NC_000007.13 - 143016166	Oct 12, 2018 (152)
79	A Vietnamese Genetic Variation Database	NC_000007.13 - 143016166	Jul 13, 2019 (153)
80	ALFA	NC_000007.14 - 143319073	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)
rs56911934	May 23, 2008 (130)
rs59283934	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss85547893	NC_000007.11:142533002:G:A	NC_000007.14:143319072:G:A	(self)
ss66460997, ss76259638, ss114565977, ss116355630, ss165578869, ss173011244, ss198414957, ss208298657, ss254732104, ss279566743, ss1594490221, ss1712994650	NC_000007.12:142726287:G:A	NC_000007.14:143319072:G:A	(self)
39582934, 22031081, 421904, 15688140, 8605269, 9828466, 23161326, 8440502, 10198689, 20616087, 5509541, 43997818, 22031081, 4904530, ss223382296, ss234203736, ss560362899, ss654776052, ss984900695, ss1075056817, ss1327524749, ss1431308832, ss1582440331, ss1619424662, ss1662418695, ss1805265904, ss1928156759, ss1970838527, ss2024767982, ss2152993187, ss2708716268, ss2860223641, ss3002202006, ss3347889724, ss3669949892, ss3735155637, ss3767280077, ss3830869713, ss3868599107, ss3915983932, ss5186028511, ss5377412118, ss5644181200, ss5823658549, ss5973387847	NC_000007.13:143016165:G:A	NC_000007.14:143319072:G:A	(self)
51946733, 279524610, 3512753, 19146179, 61009390, 604537928, 11667732787, ss2298656148, ss3026173538, ss3720886605, ss3810442355, ss3962768178, ss4767160369, ss5275088149, ss5471934786, ss5564420798, ss5727172286, ss5809182848, ss5856135746, ss5861281560	NC_000007.14:143319072:G:A	NC_000007.14:143319072:G:A	(self)
ss14144254	NT_007914.13:3671370:G:A	NC_000007.14:143319072:G:A	(self)
ss82713380	NT_007914.15:3611788:G:A	NC_000007.14:143319072:G: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 rs10274425

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

rs10274425