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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.

rs200503540

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:17452 (GRCh38.p13) 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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.004052 (534/131776, GnomAD)
T=0.034914 (4437/127082, GnomAD_exome)
T=0.03242 (789/24336, ALFA) (+ 7 more)
T=0.01623 (272/16758, 8.3KJPN)
T=0.07754 (988/12742, ExAC)
T=0.0154 (45/2922, KOREAN)
T=0.0049 (9/1832, Korea1K)
T=0.069 (15/216, Qatari)
C=0.5 (3/6, Siberian)
T=0.5 (3/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MIR6859-1 : 2KB Upstream Variant
WASH7P : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.17452C>A
GRCh38.p13 chr 1 NC_000001.11:g.17452C>T
GRCh37.p13 chr 1 NC_000001.10:g.17452C>A
GRCh37.p13 chr 1 NC_000001.10:g.17452C>T
Gene: WASH7P, WASP family homolog 7, pseudogene (minus strand)
Molecule type Change Amino acid[Codon] SO Term
WASH7P transcript NR_024540.1:n. N/A Intron Variant
Gene: MIR6859-1, microRNA 6859-1 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR6859-1 transcript NR_106918.1:n. N/A Upstream Transcript 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 24336 C=0.96758 A=0.00000, T=0.03242
European Sub 17568 C=0.96795 A=0.00000, T=0.03205
African Sub 3156 C=0.9873 A=0.0000, T=0.0127
African Others Sub 104 C=0.990 A=0.000, T=0.010
African American Sub 3052 C=0.9872 A=0.0000, T=0.0128
Asian Sub 156 C=0.987 A=0.000, T=0.013
East Asian Sub 106 C=0.991 A=0.000, T=0.009
Other Asian Sub 50 C=0.98 A=0.00, T=0.02
Latin American 1 Sub 130 C=1.000 A=0.000, T=0.000
Latin American 2 Sub 520 C=1.000 A=0.000, T=0.000
South Asian Sub 94 C=1.00 A=0.00, T=0.00
Other Sub 2712 C=0.9322 A=0.0000, T=0.0678


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
gnomAD - Genomes Global Study-wide 131776 C=0.995948 T=0.004052
gnomAD - Genomes European Sub 71760 C=0.99681 T=0.00319
gnomAD - Genomes African Sub 39004 C=0.99418 T=0.00582
gnomAD - Genomes American Sub 12702 C=0.99504 T=0.00496
gnomAD - Genomes Ashkenazi Jewish Sub 3194 C=0.9987 T=0.0013
gnomAD - Genomes East Asian Sub 3094 C=0.9994 T=0.0006
gnomAD - Genomes Other Sub 2022 C=0.9955 T=0.0045
gnomAD - Exomes Global Study-wide 127082 C=0.965086 T=0.034914
gnomAD - Exomes European Sub 61788 C=0.97046 T=0.02954
gnomAD - Exomes Asian Sub 30278 C=0.98388 T=0.01612
gnomAD - Exomes American Sub 18576 C=0.91128 T=0.08872
gnomAD - Exomes Ashkenazi Jewish Sub 6982 C=0.9798 T=0.0202
gnomAD - Exomes African Sub 5940 C=0.9653 T=0.0347
gnomAD - Exomes Other Sub 3518 C=0.9633 T=0.0367
8.3KJPN JAPANESE Study-wide 16758 C=0.98377 T=0.01623
ExAC Global Study-wide 12742 C=0.92246 T=0.07754
ExAC Europe Sub 6028 C=0.9038 T=0.0962
ExAC Asian Sub 5062 C=0.9561 T=0.0439
ExAC African Sub 1144 C=0.8977 T=0.1023
ExAC American Sub 368 C=0.853 T=0.147
ExAC Other Sub 140 C=0.893 T=0.107
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9846 T=0.0154
Korean Genome Project KOREAN Study-wide 1832 C=0.9951 T=0.0049
Qatari Global Study-wide 216 C=0.931 T=0.069
Siberian Global Study-wide 6 C=0.5 T=0.5
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 C= A T
GRCh38.p13 chr 1 NC_000001.11:g.17452= NC_000001.11:g.17452C>A NC_000001.11:g.17452C>T
GRCh37.p13 chr 1 NC_000001.10:g.17452= NC_000001.10:g.17452C>A NC_000001.10:g.17452C>T
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#.

17 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 CLINSEQ_SNP ss491581586 May 04, 2012 (137)
2 BILGI_BIOE ss538305548 Apr 25, 2013 (138)
3 SSMP ss647514757 Apr 25, 2013 (138)
4 EVA_EXAC ss1685216861 Apr 01, 2015 (144)
5 WEILL_CORNELL_DGM ss1917958137 Feb 12, 2016 (147)
6 USC_VALOUEV ss2147483692 Dec 20, 2016 (150)
7 GRF ss2697372911 Nov 08, 2017 (151)
8 GNOMAD ss2746168707 Nov 08, 2017 (151)
9 GNOMAD ss2750601993 Nov 08, 2017 (151)
10 SWEGEN ss2986141485 Nov 08, 2017 (151)
11 TOPMED ss3066317579 Nov 08, 2017 (151)
12 TOPMED ss3066317580 Nov 08, 2017 (151)
13 CSHL ss3343271478 Nov 08, 2017 (151)
14 KRGDB ss3892823084 Apr 25, 2020 (154)
15 KOGIC ss3943622220 Apr 25, 2020 (154)
16 EVA ss5141868162 Apr 25, 2021 (155)
17 TOMMO_GENOMICS ss5142031542 Apr 25, 2021 (155)
18 ExAC NC_000001.10 - 17452 Oct 11, 2018 (152)
19 gnomAD - Genomes NC_000001.11 - 17452 Apr 25, 2021 (155)
20 gnomAD - Exomes NC_000001.10 - 17452 Jul 12, 2019 (153)
21 KOREAN population from KRGDB NC_000001.10 - 17452 Apr 25, 2020 (154)
22 Korean Genome Project NC_000001.11 - 17452 Apr 25, 2020 (154)
23 Qatari NC_000001.10 - 17452 Apr 25, 2020 (154)
24 Siberian NC_000001.10 - 17452 Apr 25, 2020 (154)
25 8.3KJPN NC_000001.10 - 17452 Apr 25, 2021 (155)
26 ALFA NC_000001.11 - 17452 Apr 25, 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
10962566254, ss3066317579 NC_000001.11:17451:C:A NC_000001.11:17451:C:A (self)
ss491581586 NC_000001.9:7314:C:T NC_000001.11:17451:C:T (self)
4389932, 75, 478, 67, 46, 849, ss538305548, ss647514757, ss1685216861, ss1917958137, ss2147483692, ss2697372911, ss2746168707, ss2750601993, ss2986141485, ss3343271478, ss3892823084, ss5142031542 NC_000001.10:17451:C:T NC_000001.11:17451:C:T (self)
1683, 221, 10962566254, ss3066317580, ss3943622220, ss5141868162 NC_000001.11:17451:C:T NC_000001.11:17451:C:T (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 rs200503540

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.post596+ae089ad