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dbSNP Short Genetic Variations

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.

rs188212225

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrX:50095889 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.00027 (6/22223, 14KJPN)
G=0.00000 (0/14050, ALFA)
G=0.00031 (4/12843, 8.3KJPN) (+ 2 more)
G=0.0002 (1/4805, 1000G_30x)
G=0.0003 (1/3775, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CLCN5 : 3 Prime UTR 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 14050 A=1.00000 G=0.00000
European Sub 9690 A=1.0000 G=0.0000
African Sub 2898 A=1.0000 G=0.0000
African Others Sub 114 A=1.000 G=0.000
African American Sub 2784 A=1.0000 G=0.0000
Asian Sub 112 A=1.000 G=0.000
East Asian Sub 86 A=1.00 G=0.00
Other Asian Sub 26 A=1.00 G=0.00
Latin American 1 Sub 146 A=1.000 G=0.000
Latin American 2 Sub 610 A=1.000 G=0.000
South Asian Sub 98 A=1.00 G=0.00
Other Sub 496 A=1.000 G=0.000


Help

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
14KJPN JAPANESE Study-wide 22223 A=0.99973 G=0.00027
Allele Frequency Aggregator Total Global 14050 A=1.00000 G=0.00000
Allele Frequency Aggregator European Sub 9690 A=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 2898 A=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 G=0.000
Allele Frequency Aggregator Other Sub 496 A=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 112 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 G=0.00
8.3KJPN JAPANESE Study-wide 12843 A=0.99969 G=0.00031
1000Genomes_30x Global Study-wide 4805 A=0.9998 G=0.0002
1000Genomes_30x African Sub 1328 A=1.0000 G=0.0000
1000Genomes_30x Europe Sub 961 A=1.000 G=0.000
1000Genomes_30x South Asian Sub 883 A=1.000 G=0.000
1000Genomes_30x East Asian Sub 878 A=0.999 G=0.001
1000Genomes_30x American Sub 755 A=1.000 G=0.000
1000Genomes Global Study-wide 3775 A=0.9997 G=0.0003
1000Genomes African Sub 1003 A=1.0000 G=0.0000
1000Genomes Europe Sub 766 A=1.000 G=0.000
1000Genomes East Asian Sub 764 A=0.999 G=0.001
1000Genomes South Asian Sub 718 A=1.000 G=0.000
1000Genomes American Sub 524 A=1.000 G=0.000
Help

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 X NC_000023.11:g.50095889A>G
GRCh37.p13 chr X fix patch HG1436_HG1432_PATCH NW_004070880.2:g.2285318A>G
CLCN5 RefSeqGene NG_007159.3:g.178274A>G
GRCh37.p13 chr X NC_000023.10:g.49860546A>G
Gene: CLCN5, chloride voltage-gated channel 5 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CLCN5 transcript variant 2 NM_001127898.4:c.*3670= N/A 3 Prime UTR Variant
CLCN5 transcript variant 3 NM_000084.5:c.*3670= N/A 3 Prime UTR Variant
CLCN5 transcript variant 1 NM_001127899.4:c.*3670= N/A 3 Prime UTR Variant
CLCN5 transcript variant 4 NM_001282163.2:c.*3670= N/A 3 Prime UTR Variant
CLCN5 transcript variant 5 NM_001272102.2:c. N/A Genic Downstream Transcript Variant
CLCN5 transcript variant X1 XM_017029258.2:c.*3670= N/A 3 Prime UTR Variant
CLCN5 transcript variant X2 XM_017029257.2:c.*3670= N/A 3 Prime UTR Variant
CLCN5 transcript variant X3 XM_047441807.1:c.*3670= N/A 3 Prime UTR Variant
CLCN5 transcript variant X4 XM_047441808.1:c.*3670= N/A 3 Prime UTR Variant
Help

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
Help

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 A= G
GRCh38.p14 chr X NC_000023.11:g.50095889= NC_000023.11:g.50095889A>G
GRCh37.p13 chr X fix patch HG1436_HG1432_PATCH NW_004070880.2:g.2285318= NW_004070880.2:g.2285318A>G
CLCN5 RefSeqGene NG_007159.3:g.178274= NG_007159.3:g.178274A>G
CLCN5 transcript variant 3 NM_000084.5:c.*3670= NM_000084.5:c.*3670A>G
CLCN5 transcript variant 3 NM_000084.4:c.*3670= NM_000084.4:c.*3670A>G
CLCN5 transcript variant 3 NM_000084.3:c.*3670= NM_000084.3:c.*3670A>G
CLCN5 transcript variant 1 NM_001127899.4:c.*3670= NM_001127899.4:c.*3670A>G
CLCN5 transcript variant 1 NM_001127899.3:c.*3670= NM_001127899.3:c.*3670A>G
CLCN5 transcript variant 1 NM_001127899.2:c.*3670= NM_001127899.2:c.*3670A>G
CLCN5 transcript variant 2 NM_001127898.4:c.*3670= NM_001127898.4:c.*3670A>G
CLCN5 transcript variant 2 NM_001127898.3:c.*3670= NM_001127898.3:c.*3670A>G
CLCN5 transcript variant 2 NM_001127898.2:c.*3670= NM_001127898.2:c.*3670A>G
CLCN5 transcript variant 4 NM_001282163.2:c.*3670= NM_001282163.2:c.*3670A>G
CLCN5 transcript variant 4 NM_001282163.1:c.*3670= NM_001282163.1:c.*3670A>G
GRCh37.p13 chr X NC_000023.10:g.49860546= NC_000023.10:g.49860546A>G
CLCN5 transcript variant X1 XM_017029258.2:c.*3670= XM_017029258.2:c.*3670A>G
CLCN5 transcript variant X2 XM_017029258.1:c.*3670= XM_017029258.1:c.*3670A>G
CLCN5 transcript variant X2 XM_017029257.2:c.*3670= XM_017029257.2:c.*3670A>G
CLCN5 transcript variant X1 XM_017029257.1:c.*3670= XM_017029257.1:c.*3670A>G
CLCN5 transcript variant X4 XM_047441808.1:c.*3670= XM_047441808.1:c.*3670A>G
CLCN5 transcript variant 4 NR_073607.1:n.6202= NR_073607.1:n.6202A>G
CLCN5 transcript variant X3 XM_047441807.1:c.*3670= XM_047441807.1:c.*3670A>G
Help

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#.

5 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss466504873 Sep 17, 2011 (135)
2 1000GENOMES ss1554378274 Apr 09, 2015 (144)
3 TOMMO_GENOMICS ss5234408511 Apr 26, 2021 (155)
4 1000G_HIGH_COVERAGE ss5620708519 Oct 16, 2022 (156)
5 TOMMO_GENOMICS ss5796100031 Oct 16, 2022 (156)
6 1000Genomes NC_000023.10 - 49860546 Oct 13, 2018 (152)
7 1000Genomes_30x NC_000023.11 - 50095889 Oct 16, 2022 (156)
8 8.3KJPN NC_000023.10 - 49860546 Apr 26, 2021 (155)
9 14KJPN NC_000023.11 - 50095889 Oct 16, 2022 (156)
10 ALFA NC_000023.11 - 50095889 Apr 26, 2021 (155)
Help

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
82353724, 92377818, ss466504873, ss1554378274, ss5234408511 NC_000023.10:49860545:A:G NC_000023.11:50095888:A:G (self)
108234454, 129937135, 7437828633, ss5620708519, ss5796100031 NC_000023.11:50095888:A:G NC_000023.11:50095888:A:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs188212225

Help

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.

Software version is: 2.0.1.post761+d5e8e07