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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.

rs2821574

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr21:13015459 (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
A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000014 (2/140340, GnomAD)
T=0.00059 (11/18520, ALFA)
T=0.00018 (3/16760, 8.3KJPN)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 21 NC_000021.9:g.13015459A>G
GRCh38.p13 chr 21 NC_000021.9:g.13015459A>T
GRCh37.p13 chr 21 NC_000021.8:g.14387780A>G
GRCh37.p13 chr 21 NC_000021.8:g.14387780A>T
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 18520 A=0.99941 G=0.00000, T=0.00059
European Sub 14152 A=0.99922 G=0.00000, T=0.00078
African Sub 2898 A=1.0000 G=0.0000, T=0.0000
African Others Sub 114 A=1.000 G=0.000, T=0.000
African American Sub 2784 A=1.0000 G=0.0000, T=0.0000
Asian Sub 112 A=1.000 G=0.000, T=0.000
East Asian Sub 86 A=1.00 G=0.00, T=0.00
Other Asian Sub 26 A=1.00 G=0.00, T=0.00
Latin American 1 Sub 146 A=1.000 G=0.000, T=0.000
Latin American 2 Sub 610 A=1.000 G=0.000, T=0.000
South Asian Sub 98 A=1.00 G=0.00, T=0.00
Other Sub 504 A=1.000 G=0.000, T=0.000


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 140340 A=0.999986 G=0.000014
gnomAD - Genomes European Sub 75980 A=1.00000 G=0.00000
gnomAD - Genomes African Sub 42078 A=0.99995 G=0.00005
gnomAD - Genomes American Sub 13670 A=1.00000 G=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3134 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2154 A=1.0000 G=0.0000
Allele Frequency Aggregator Total Global 18520 A=0.99941 G=0.00000, T=0.00059
Allele Frequency Aggregator European Sub 14152 A=0.99922 G=0.00000, T=0.00078
Allele Frequency Aggregator African Sub 2898 A=1.0000 G=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Other Sub 504 A=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 112 A=1.000 G=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 G=0.00, T=0.00
8.3KJPN JAPANESE Study-wide 16760 A=0.99982 T=0.00018
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 A= G T
GRCh38.p13 chr 21 NC_000021.9:g.13015459= NC_000021.9:g.13015459A>G NC_000021.9:g.13015459A>T
GRCh37.p13 chr 21 NC_000021.8:g.14387780= NC_000021.8:g.14387780A>G NC_000021.8:g.14387780A>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#.

14 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2411554 Oct 08, 2002 (110)
2 PERLEGEN ss3995631 Sep 28, 2001 (100)
3 TSC-CSHL ss5169108 Oct 08, 2002 (110)
4 TSC-CSHL ss5409599 Oct 08, 2002 (110)
5 TSC-CSHL ss5443155 Oct 08, 2002 (110)
6 SC_JCM ss5974197 Feb 20, 2003 (111)
7 WI_SSAHASNP ss6652899 Feb 20, 2003 (111)
8 BCM_SSAHASNP ss10985026 Jul 11, 2003 (117)
9 SC_SNP ss13401127 Dec 05, 2003 (119)
10 SC_SNP ss14785334 Dec 05, 2003 (119)
11 GNOMAD ss2969711629 Nov 08, 2017 (151)
12 TOPMED ss3366034719 Nov 08, 2017 (151)
13 TOPMED ss3366034720 Nov 08, 2017 (151)
14 TOMMO_GENOMICS ss5230695663 Apr 26, 2021 (155)
15 gnomAD - Genomes NC_000021.9 - 13015459 Apr 26, 2021 (155)
16 8.3KJPN NC_000021.8 - 14387780 Apr 26, 2021 (155)
17 ALFA NC_000021.9 - 13015459 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).

Associated ID History Updated (Build)
rs3868215 Dec 16, 2002 (110)
rs7280156 Aug 27, 2003 (117)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
557940677, 1008233204, ss3366034719 NC_000021.9:13015458:A:G NC_000021.9:13015458:A:G (self)
88664970, ss2969711629, ss5230695663 NC_000021.8:14387779:A:T NC_000021.9:13015458:A:T (self)
231256594, 1008233204, ss3366034720 NC_000021.9:13015458:A:T NC_000021.9:13015458:A:T (self)
ss10985026 NT_011512.8:49650:A:T NC_000021.9:13015458:A:T (self)
ss2411554, ss3995631, ss5169108, ss5409599, ss5443155, ss5974197, ss6652899, ss13401127, ss14785334 NT_011512.11:49650:A:T NC_000021.9:13015458:A: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 rs2821574

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