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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.

rs200850333

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:633366-633367 (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
dupCA
Variation Type
Indel Insertion and Deletion
Frequency
dupCA=0.35032 (5671/16188, ALFA)
dupCA=0.04959 (729/14700, 8.3KJPN)
dupCA=0.0320 (52/1626, Korea1K) (+ 1 more)
dupCA=0.045 (9/202, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MIR12136 : 2KB Upstream 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.633366_633367dup
GRCh37.p13 chr 1 NC_000001.10:g.568746_568747dup
MTCO2P12 pseudogene NG_046448.1:g.710_711dup
Gene: MIR12136, microRNA 12136 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR12136 transcript NR_162149.1: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 16188 CA=0.64968 CACA=0.35032
European Sub 11936 CA=0.72068 CACA=0.27932
African Sub 2816 CA=0.2955 CACA=0.7045
African Others Sub 108 CA=0.157 CACA=0.843
African American Sub 2708 CA=0.3010 CACA=0.6990
Asian Sub 108 CA=0.944 CACA=0.056
East Asian Sub 84 CA=0.94 CACA=0.06
Other Asian Sub 24 CA=0.96 CACA=0.04
Latin American 1 Sub 146 CA=0.623 CACA=0.377
Latin American 2 Sub 610 CA=0.823 CACA=0.177
South Asian Sub 94 CA=0.72 CACA=0.28
Other Sub 478 CA=0.669 CACA=0.331


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
8.3KJPN JAPANESE Study-wide 14700 -

No frequency provided

dupCA=0.04959
Korean Genome Project KOREAN Study-wide 1626 -

No frequency provided

dupCA=0.0320
A Vietnamese Genetic Variation Database Global Study-wide 202 -

No frequency provided

dupCA=0.045
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 CA= dupCA
GRCh38.p13 chr 1 NC_000001.11:g.633366_633367= NC_000001.11:g.633366_633367dup
GRCh37.p13 chr 1 NC_000001.10:g.568746_568747= NC_000001.10:g.568746_568747dup
MTCO2P12 pseudogene NG_046448.1:g.710_711= NG_046448.1:g.710_711dup
MTCO2 transcript NM_173705.1:c.610_613= NM_173705.1:c.612_613dup
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#.

15 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss498763782 May 04, 2012 (137)
2 SSMP ss663194407 Apr 01, 2015 (144)
3 BILGI_BIOE ss666079967 Apr 25, 2013 (138)
4 HAMMER_LAB ss1793705353 Sep 08, 2015 (146)
5 SYSTEMSBIOZJU ss2624264689 Nov 08, 2017 (151)
6 GNOMAD ss2750623347 Nov 08, 2017 (151)
7 SWEGEN ss2986145924 Nov 08, 2017 (151)
8 MCHAISSO ss3063573461 Nov 08, 2017 (151)
9 MCHAISSO ss3064385979 Nov 08, 2017 (151)
10 MCHAISSO ss3065282456 Nov 08, 2017 (151)
11 TOPMED ss3066367987 Nov 08, 2017 (151)
12 EVA_DECODE ss3685991350 Jul 12, 2019 (153)
13 EVA ss3825981361 Apr 25, 2020 (154)
14 KOGIC ss3943626748 Apr 25, 2020 (154)
15 TOMMO_GENOMICS ss5142044347 Apr 25, 2021 (155)
16 Korean Genome Project NC_000001.11 - 633366 Apr 25, 2020 (154)
17 8.3KJPN NC_000001.10 - 568746 Apr 25, 2021 (155)
18 A Vietnamese Genetic Variation Database NC_000001.10 - 568746 Jul 12, 2019 (153)
19 ALFA NC_000001.11 - 633366 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
13654, 10, ss498763782, ss663194407, ss666079967, ss1793705353, ss2624264689, ss2750623347, ss2986145924, ss3825981361, ss5142044347 NC_000001.10:568745::CA NC_000001.11:633365:CA:CACA (self)
4749, ss3063573461, ss3064385979, ss3065282456, ss3066367987, ss3685991350, ss3943626748 NC_000001.11:633365::CA NC_000001.11:633365:CA:CACA (self)
4765532769 NC_000001.11:633365:CA:CACA NC_000001.11:633365:CA:CACA
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 rs200850333

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