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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.

rs1488347609

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr19:12671032-12671043 (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
delAAT
Variation Type
Indel Insertion and Deletion
Frequency
delAAT=0.000011 (3/264690, TOPMED)
delAAT=0.000007 (1/140206, GnomAD)
delAAT=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
WDR83 : Intron Variant
WDR83OS : 2KB Upstream 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 14050 AATAATAATAAT=1.00000 AATAATAAT=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 AATAATAATAAT=1.0000 AATAATAAT=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 AATAATAATAAT=1.0000 AATAATAAT=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 AATAATAATAAT=1.000 AATAATAAT=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 AATAATAATAAT=1.0000 AATAATAAT=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 AATAATAATAAT=1.000 AATAATAAT=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 AATAATAATAAT=1.00 AATAATAAT=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 AATAATAATAAT=1.00 AATAATAAT=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 AATAATAATAAT=1.000 AATAATAAT=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 AATAATAATAAT=1.000 AATAATAAT=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 AATAATAATAAT=1.00 AATAATAAT=0.00 1.0 0.0 0.0 N/A
Other Sub 496 AATAATAATAAT=1.000 AATAATAAT=0.000 1.0 0.0 0.0 N/A


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
TopMed Global Study-wide 264690 (AAT)4=0.999989 delAAT=0.000011
gnomAD - Genomes Global Study-wide 140206 (AAT)4=0.999993 delAAT=0.000007
gnomAD - Genomes European Sub 75946 (AAT)4=0.99999 delAAT=0.00001
gnomAD - Genomes African Sub 42020 (AAT)4=1.00000 delAAT=0.00000
gnomAD - Genomes American Sub 13634 (AAT)4=1.00000 delAAT=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 (AAT)4=1.0000 delAAT=0.0000
gnomAD - Genomes East Asian Sub 3132 (AAT)4=1.0000 delAAT=0.0000
gnomAD - Genomes Other Sub 2150 (AAT)4=1.0000 delAAT=0.0000
Allele Frequency Aggregator Total Global 14050 (AAT)4=1.00000 delAAT=0.00000
Allele Frequency Aggregator European Sub 9690 (AAT)4=1.0000 delAAT=0.0000
Allele Frequency Aggregator African Sub 2898 (AAT)4=1.0000 delAAT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (AAT)4=1.000 delAAT=0.000
Allele Frequency Aggregator Other Sub 496 (AAT)4=1.000 delAAT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (AAT)4=1.000 delAAT=0.000
Allele Frequency Aggregator Asian Sub 112 (AAT)4=1.000 delAAT=0.000
Allele Frequency Aggregator South Asian Sub 98 (AAT)4=1.00 delAAT=0.00
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 19 NC_000019.10:g.12671032AAT[3]
GRCh37.p13 chr 19 NC_000019.9:g.12781846AAT[3]
MAN2B1 RefSeqGene NG_008318.1:g.735ATT[3]
WDR83 RefSeqGene NG_015814.1:g.9229AAT[3]
Gene: WDR83, WD repeat domain 83 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
WDR83 transcript variant 1 NM_001099737.3:c.506+211A…

NM_001099737.3:c.506+211AAT[3]

N/A Intron Variant
WDR83 transcript variant 2 NM_032332.4:c.506+211AAT[…

NM_032332.4:c.506+211AAT[3]

N/A Intron Variant
WDR83 transcript variant 3 NR_029375.2:n. N/A Intron Variant
Gene: WDR83OS, WD repeat domain 83 opposite strand (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
WDR83OS transcript NM_016145.4:c. 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
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 (AAT)4= delAAT
GRCh38.p14 chr 19 NC_000019.10:g.12671032_12671043= NC_000019.10:g.12671032AAT[3]
GRCh37.p13 chr 19 NC_000019.9:g.12781846_12781857= NC_000019.9:g.12781846AAT[3]
MAN2B1 RefSeqGene NG_008318.1:g.735_746= NG_008318.1:g.735ATT[3]
WDR83 RefSeqGene NG_015814.1:g.9229_9240= NG_015814.1:g.9229AAT[3]
WDR83 transcript variant 1 NM_001099737.2:c.506+211= NM_001099737.2:c.506+211AAT[3]
WDR83 transcript variant 1 NM_001099737.3:c.506+211= NM_001099737.3:c.506+211AAT[3]
WDR83 transcript variant 2 NM_032332.3:c.506+211= NM_032332.3:c.506+211AAT[3]
WDR83 transcript variant 2 NM_032332.4:c.506+211= NM_032332.4:c.506+211AAT[3]
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#.

2 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss4327946213 Apr 26, 2021 (155)
2 TOPMED ss5068520519 Apr 26, 2021 (155)
3 gnomAD - Genomes NC_000019.10 - 12671032 Apr 26, 2021 (155)
4 TopMed NC_000019.10 - 12671032 Apr 26, 2021 (155)
5 ALFA NC_000019.10 - 12671032 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
534560470, 284066183, ss4327946213, ss5068520519 NC_000019.10:12671031:AAT: NC_000019.10:12671031:AATAATAATAAT…

NC_000019.10:12671031:AATAATAATAAT:AATAATAAT

(self)
13192298212 NC_000019.10:12671031:AATAATAATAAT…

NC_000019.10:12671031:AATAATAATAAT:AATAATAAT

NC_000019.10:12671031:AATAATAATAAT…

NC_000019.10:12671031:AATAATAATAAT:AATAATAAT

(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 rs1488347609

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.post820+afb47a3d