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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.

rs201824320

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:114829-114831 (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
delA
Variation Type
Indel Insertion and Deletion
Frequency
delA=0.14419 (2416/16756, 8.3KJPN)
delA=0.00994 (162/16302, ALFA)
delA=0.0064 (32/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC100996442 : 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.114831del
GRCh37.p13 chr 1 NC_000001.10:g.114831del
Gene: LOC100996442, uncharacterized LOC100996442 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC100996442 transcript variant X4 XR_001737578.2:n. N/A Intron Variant
LOC100996442 transcript variant X8 XR_001737580.2:n. N/A Intron Variant
LOC100996442 transcript variant X11 XR_001737581.2:n. N/A Intron Variant
LOC100996442 transcript variant X12 XR_001737582.2:n. N/A Intron Variant
LOC100996442 transcript variant X13 XR_001737583.2:n. N/A Intron Variant
LOC100996442 transcript variant X14 XR_001737584.2:n. N/A Intron Variant
LOC100996442 transcript variant X5 XR_001737579.2:n. N/A Genic Downstream Transcript Variant
LOC100996442 transcript variant X1 XR_002958514.1:n. N/A Genic Downstream Transcript Variant
LOC100996442 transcript variant X2 XR_002958515.1:n. N/A Genic Downstream Transcript Variant
LOC100996442 transcript variant X3 XR_002958516.1:n. N/A Genic Downstream Transcript Variant
LOC100996442 transcript variant X6 XR_002958517.1:n. N/A Genic Downstream Transcript Variant
LOC100996442 transcript variant X7 XR_002958518.1:n. N/A Genic Downstream Transcript Variant
LOC100996442 transcript variant X9 XR_002958519.1:n. N/A Genic Downstream Transcript Variant
LOC100996442 transcript variant X10 XR_002958520.1:n. N/A Genic Downstream 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 16302 AAA=0.99006 AA=0.00994
European Sub 12050 AAA=0.99577 AA=0.00423
African Sub 2816 AAA=0.9830 AA=0.0170
African Others Sub 108 AAA=0.981 AA=0.019
African American Sub 2708 AAA=0.9830 AA=0.0170
Asian Sub 108 AAA=0.824 AA=0.176
East Asian Sub 84 AAA=0.83 AA=0.17
Other Asian Sub 24 AAA=0.79 AA=0.21
Latin American 1 Sub 146 AAA=0.993 AA=0.007
Latin American 2 Sub 610 AAA=0.977 AA=0.023
South Asian Sub 94 AAA=0.89 AA=0.11
Other Sub 478 AAA=0.960 AA=0.040


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 16756 AAA=0.85581 delA=0.14419
1000Genomes Global Study-wide 5008 AAA=0.9936 delA=0.0064
1000Genomes African Sub 1322 AAA=0.9977 delA=0.0023
1000Genomes East Asian Sub 1008 AAA=0.9802 delA=0.0198
1000Genomes Europe Sub 1006 AAA=1.0000 delA=0.0000
1000Genomes South Asian Sub 978 AAA=0.994 delA=0.006
1000Genomes American Sub 694 AAA=0.996 delA=0.004
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 AAA= delA
GRCh38.p13 chr 1 NC_000001.11:g.114829_114831= NC_000001.11:g.114831del
GRCh37.p13 chr 1 NC_000001.10:g.114829_114831= NC_000001.10:g.114831del
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#.

7 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss498763769 May 04, 2012 (137)
2 1000GENOMES ss1367645238 Aug 21, 2014 (142)
3 GNOMAD ss2750609584 Nov 08, 2017 (151)
4 SWEGEN ss2986143089 Nov 08, 2017 (151)
5 TOPMED ss3066333636 Nov 08, 2017 (151)
6 EVA_DECODE ss3685990800 Jul 12, 2019 (153)
7 TOMMO_GENOMICS ss5142036174 Apr 25, 2021 (155)
8 1000Genomes NC_000001.10 - 114829 Oct 11, 2018 (152)
9 8.3KJPN NC_000001.10 - 114829 Apr 25, 2021 (155)
10 ALFA NC_000001.11 - 114829 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
894, 5481, ss498763769, ss1367645238, ss2750609584, ss2986143089, ss5142036174 NC_000001.10:114828:A: NC_000001.11:114828:AAA:AA (self)
ss3066333636, ss3685990800 NC_000001.11:114828:A: NC_000001.11:114828:AAA:AA (self)
10788137433 NC_000001.11:114828:AAA:AA NC_000001.11:114828:AAA:AA
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 rs201824320

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