Name: rs201840291
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.

rs201840291

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:50093759-50093767 (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: delA / dupA
Variation Type: Indel Insertion and Deletion
Frequency: dupA=0.000586 (155/264690, TOPMED)
dupA=0.00040 (9/22223, 14KJPN)
delA=0.00000 (0/14048, ALFA) (+ 3 more)
dupA=0.00000 (0/14048, ALFA)
dupA=0.00023 (3/12843, 8.3KJPN)
dupA=0.0006 (3/4805, 1000G_30x)

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	14048	AAAAAAAAA=1.00000	AAAAAAAA=0.00000, AAAAAAAAAA=0.00000
European	Sub	9688	AAAAAAAAA=1.0000	AAAAAAAA=0.0000, AAAAAAAAAA=0.0000
African	Sub	2898	AAAAAAAAA=1.0000	AAAAAAAA=0.0000, AAAAAAAAAA=0.0000
African Others	Sub	114	AAAAAAAAA=1.000	AAAAAAAA=0.000, AAAAAAAAAA=0.000
African American	Sub	2784	AAAAAAAAA=1.0000	AAAAAAAA=0.0000, AAAAAAAAAA=0.0000
Asian	Sub	112	AAAAAAAAA=1.000	AAAAAAAA=0.000, AAAAAAAAAA=0.000
East Asian	Sub	86	AAAAAAAAA=1.00	AAAAAAAA=0.00, AAAAAAAAAA=0.00
Other Asian	Sub	26	AAAAAAAAA=1.00	AAAAAAAA=0.00, AAAAAAAAAA=0.00
Latin American 1	Sub	146	AAAAAAAAA=1.000	AAAAAAAA=0.000, AAAAAAAAAA=0.000
Latin American 2	Sub	610	AAAAAAAAA=1.000	AAAAAAAA=0.000, AAAAAAAAAA=0.000
South Asian	Sub	98	AAAAAAAAA=1.00	AAAAAAAA=0.00, AAAAAAAAAA=0.00
Other	Sub	496	AAAAAAAAA=1.000	AAAAAAAA=0.000, AAAAAAAAAA=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	- No frequency provided	dupA=0.000586
14KJPN	JAPANESE	Study-wide	22223	- No frequency provided	dupA=0.00040
Allele Frequency Aggregator	Total	Global	14048	(A)₉=1.00000	delA=0.00000, dupA=0.00000
Allele Frequency Aggregator	European	Sub	9688	(A)₉=1.0000	delA=0.0000, dupA=0.0000
Allele Frequency Aggregator	African	Sub	2898	(A)₉=1.0000	delA=0.0000, dupA=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(A)₉=1.000	delA=0.000, dupA=0.000
Allele Frequency Aggregator	Other	Sub	496	(A)₉=1.000	delA=0.000, dupA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(A)₉=1.000	delA=0.000, dupA=0.000
Allele Frequency Aggregator	Asian	Sub	112	(A)₉=1.000	delA=0.000, dupA=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(A)₉=1.00	delA=0.00, dupA=0.00
8.3KJPN	JAPANESE	Study-wide	12843	- No frequency provided	dupA=0.00023
1000Genomes_30x	Global	Study-wide	4805	- No frequency provided	dupA=0.0006
1000Genomes_30x	African	Sub	1328	- No frequency provided	dupA=0.0000
1000Genomes_30x	Europe	Sub	961	- No frequency provided	dupA=0.002
1000Genomes_30x	South Asian	Sub	883	- No frequency provided	dupA=0.001
1000Genomes_30x	East Asian	Sub	878	- No frequency provided	dupA=0.000
1000Genomes_30x	American	Sub	755	- No frequency provided	dupA=0.000

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.50093767del
GRCh38.p14 chr X	NC_000023.11:g.50093767dup
GRCh37.p13 chr X fix patch HG1436_HG1432_PATCH	NW_004070880.2:g.2283196del
GRCh37.p13 chr X fix patch HG1436_HG1432_PATCH	NW_004070880.2:g.2283196dup
CLCN5 RefSeqGene	NG_007159.3:g.176152del
CLCN5 RefSeqGene	NG_007159.3:g.176152dup
GRCh37.p13 chr X	NC_000023.10:g.49858424del
GRCh37.p13 chr X	NC_000023.10:g.49858424dup

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.1540_1… NM_001127898.4:c.1540_1548=	N/A	3 Prime UTR Variant
CLCN5 transcript variant 3	NM_000084.5:c.1540_1548=	N/A	3 Prime UTR Variant
CLCN5 transcript variant 1	NM_001127899.4:c.1540_1… NM_001127899.4:c.1540_1548=	N/A	3 Prime UTR Variant
CLCN5 transcript variant 4	NM_001282163.2:c.1540_1… NM_001282163.2:c.1540_1548=	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.1540_1… XM_017029258.2:c.1540_1548=	N/A	3 Prime UTR Variant
CLCN5 transcript variant X2	XM_017029257.2:c.1540_1… XM_017029257.2:c.1540_1548=	N/A	3 Prime UTR Variant
CLCN5 transcript variant X3	XM_047441807.1:c.1540_1… XM_047441807.1:c.1540_1548=	N/A	3 Prime UTR Variant
CLCN5 transcript variant X4	XM_047441808.1:c.1540_1… XM_047441808.1:c.1540_1548=	N/A	3 Prime UTR 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	(A)₉=	delA	dupA
GRCh38.p14 chr X	NC_000023.11:g.50093759_50093767=	NC_000023.11:g.50093767del	NC_000023.11:g.50093767dup
GRCh37.p13 chr X fix patch HG1436_HG1432_PATCH	NW_004070880.2:g.2283188_2283196=	NW_004070880.2:g.2283196del	NW_004070880.2:g.2283196dup
CLCN5 RefSeqGene	NG_007159.3:g.176144_176152=	NG_007159.3:g.176152del	NG_007159.3:g.176152dup
CLCN5 transcript variant 3	NM_000084.5:c.1540_1548=	NM_000084.5:c.*1548del	NM_000084.5:c.*1548dup
CLCN5 transcript variant 3	NM_000084.4:c.1540_1548=	NM_000084.4:c.*1548del	NM_000084.4:c.*1548dup
CLCN5 transcript variant 3	NM_000084.3:c.1540_1548=	NM_000084.3:c.*1548del	NM_000084.3:c.*1548dup
CLCN5 transcript variant 1	NM_001127899.4:c.1540_1548=	NM_001127899.4:c.*1548del	NM_001127899.4:c.*1548dup
CLCN5 transcript variant 1	NM_001127899.3:c.1540_1548=	NM_001127899.3:c.*1548del	NM_001127899.3:c.*1548dup
CLCN5 transcript variant 1	NM_001127899.2:c.1540_1548=	NM_001127899.2:c.*1548del	NM_001127899.2:c.*1548dup
CLCN5 transcript variant 2	NM_001127898.4:c.1540_1548=	NM_001127898.4:c.*1548del	NM_001127898.4:c.*1548dup
CLCN5 transcript variant 2	NM_001127898.3:c.1540_1548=	NM_001127898.3:c.*1548del	NM_001127898.3:c.*1548dup
CLCN5 transcript variant 2	NM_001127898.2:c.1540_1548=	NM_001127898.2:c.*1548del	NM_001127898.2:c.*1548dup
CLCN5 transcript variant 4	NM_001282163.2:c.1540_1548=	NM_001282163.2:c.*1548del	NM_001282163.2:c.*1548dup
CLCN5 transcript variant 4	NM_001282163.1:c.1540_1548=	NM_001282163.1:c.*1548del	NM_001282163.1:c.*1548dup
GRCh37.p13 chr X	NC_000023.10:g.49858416_49858424=	NC_000023.10:g.49858424del	NC_000023.10:g.49858424dup
CLCN5 transcript variant X1	XM_017029258.2:c.1540_1548=	XM_017029258.2:c.*1548del	XM_017029258.2:c.*1548dup
CLCN5 transcript variant X2	XM_017029258.1:c.1540_1548=	XM_017029258.1:c.*1548del	XM_017029258.1:c.*1548dup
CLCN5 transcript variant X2	XM_017029257.2:c.1540_1548=	XM_017029257.2:c.*1548del	XM_017029257.2:c.*1548dup
CLCN5 transcript variant X1	XM_017029257.1:c.1540_1548=	XM_017029257.1:c.*1548del	XM_017029257.1:c.*1548dup
CLCN5 transcript variant X4	XM_047441808.1:c.1540_1548=	XM_047441808.1:c.*1548del	XM_047441808.1:c.*1548dup
CLCN5 transcript variant 4	NR_073607.1:n.4072_4080=	NR_073607.1:n.4080del	NR_073607.1:n.4080dup
CLCN5 transcript variant X3	XM_047441807.1:c.1540_1548=	XM_047441807.1:c.*1548del	XM_047441807.1:c.*1548dup

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#.

10 SubSNP, 7 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss499991509	May 04, 2012 (137)
2	GNOMAD	ss4371330096	Apr 26, 2021 (155)
3	GNOMAD	ss4371330097	Apr 26, 2021 (155)
4	TOPMED	ss5122383390	Apr 26, 2021 (155)
5	TOMMO_GENOMICS	ss5234408475	Apr 26, 2021 (155)
6	1000G_HIGH_COVERAGE	ss5312501012	Oct 16, 2022 (156)
7	HUGCELL_USP	ss5504171128	Oct 16, 2022 (156)
8	1000G_HIGH_COVERAGE	ss5620708482	Oct 16, 2022 (156)
9	TOMMO_GENOMICS	ss5796099988	Oct 16, 2022 (156)
10	EVA	ss5978219509	Oct 16, 2022 (156)
11	1000Genomes_30x	NC_000023.11 - 50093759	Oct 16, 2022 (156)
12	gnomAD - Genomes Submission ignored due to conflicting rows: Row 580360754 (NC_000023.11:50093758::A 57/101782) Row 580360755 (NC_000023.11:50093758:A: 4/101774)	-	Apr 26, 2021 (155)
13	gnomAD - Genomes Submission ignored due to conflicting rows: Row 580360754 (NC_000023.11:50093758::A 57/101782) Row 580360755 (NC_000023.11:50093758:A: 4/101774)	-	Apr 26, 2021 (155)
14	8.3KJPN	NC_000023.10 - 49858416	Apr 26, 2021 (155)
15	14KJPN	NC_000023.11 - 50093759	Oct 16, 2022 (156)
16	TopMed	NC_000023.11 - 50093759	Apr 26, 2021 (155)
17	ALFA	NC_000023.11 - 50093759	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
ss4371330097	NC_000023.11:50093758:A:	NC_000023.11:50093758:AAAAAAAAA:AA… NC_000023.11:50093758:AAAAAAAAA:AAAAAAAA	(self)
9083110366	NC_000023.11:50093758:AAAAAAAAA:AA… NC_000023.11:50093758:AAAAAAAAA:AAAAAAAA	NC_000023.11:50093758:AAAAAAAAA:AA… NC_000023.11:50093758:AAAAAAAAA:AAAAAAAA	(self)
92377782, ss499991509, ss5234408475, ss5978219509	NC_000023.10:49858415::A	NC_000023.11:50093758:AAAAAAAAA:AA… NC_000023.11:50093758:AAAAAAAAA:AAAAAAAAAA	(self)
108234417, 129937092, 685989747, ss4371330096, ss5122383390, ss5312501012, ss5504171128, ss5620708482, ss5796099988	NC_000023.11:50093758::A	NC_000023.11:50093758:AAAAAAAAA:AA… NC_000023.11:50093758:AAAAAAAAA:AAAAAAAAAA	(self)
9083110366	NC_000023.11:50093758:AAAAAAAAA:AA… NC_000023.11:50093758:AAAAAAAAA:AAAAAAAAAA	NC_000023.11:50093758:AAAAAAAAA:AA… NC_000023.11:50093758:AAAAAAAAA:AAAAAAAAAA	(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 rs201840291

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

rs201840291