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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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr1:52153-52160 (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.

Variation Type
Indel Insertion and Deletion
delTAAT=0.000601 (73/121454, GnomAD)
delTAAT=0.00059 (7/11862, ALFA)
delTAAT=0.0006 (3/5008, 1000G) (+ 2 more)
delTAAT=0.0010 (4/3854, ALSPAC)
delTAAT=0.0013 (5/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
0 citations
Genomic View
See rs on genome

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.52153TAAT[1]
GRCh37.p13 chr 1 NC_000001.10:g.52153TAAT[1]

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 11862 TAATTAAT=0.99941 TAAT=0.00059
European Sub 7618 TAATTAAT=0.9991 TAAT=0.0009
African Sub 2816 TAATTAAT=1.0000 TAAT=0.0000
African Others Sub 108 TAATTAAT=1.000 TAAT=0.000
African American Sub 2708 TAATTAAT=1.0000 TAAT=0.0000
Asian Sub 108 TAATTAAT=1.000 TAAT=0.000
East Asian Sub 84 TAATTAAT=1.00 TAAT=0.00
Other Asian Sub 24 TAATTAAT=1.00 TAAT=0.00
Latin American 1 Sub 146 TAATTAAT=1.000 TAAT=0.000
Latin American 2 Sub 610 TAATTAAT=1.000 TAAT=0.000
South Asian Sub 94 TAATTAAT=1.00 TAAT=0.00
Other Sub 470 TAATTAAT=1.000 TAAT=0.000


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").

Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Genomes Global Study-wide 121454 (TAAT)2=0.999399 delTAAT=0.000601
gnomAD - Genomes European Sub 66306 (TAAT)2=0.99913 delTAAT=0.00087
gnomAD - Genomes African Sub 36546 (TAAT)2=0.99992 delTAAT=0.00008
gnomAD - Genomes American Sub 11090 (TAAT)2=0.99892 delTAAT=0.00108
gnomAD - Genomes East Asian Sub 3062 (TAAT)2=1.0000 delTAAT=0.0000
gnomAD - Genomes Ashkenazi Jewish Sub 2666 (TAAT)2=1.0000 delTAAT=0.0000
gnomAD - Genomes Other Sub 1784 (TAAT)2=1.0000 delTAAT=0.0000
Allele Frequency Aggregator Total Global 11862 (TAAT)2=0.99941 delTAAT=0.00059
Allele Frequency Aggregator European Sub 7618 (TAAT)2=0.9991 delTAAT=0.0009
Allele Frequency Aggregator African Sub 2816 (TAAT)2=1.0000 delTAAT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (TAAT)2=1.000 delTAAT=0.000
Allele Frequency Aggregator Other Sub 470 (TAAT)2=1.000 delTAAT=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (TAAT)2=1.000 delTAAT=0.000
Allele Frequency Aggregator Asian Sub 108 (TAAT)2=1.000 delTAAT=0.000
Allele Frequency Aggregator South Asian Sub 94 (TAAT)2=1.00 delTAAT=0.00
1000Genomes Global Study-wide 5008 (TAAT)2=0.9994 delTAAT=0.0006
1000Genomes African Sub 1322 (TAAT)2=0.9992 delTAAT=0.0008
1000Genomes East Asian Sub 1008 (TAAT)2=1.0000 delTAAT=0.0000
1000Genomes Europe Sub 1006 (TAAT)2=1.0000 delTAAT=0.0000
1000Genomes South Asian Sub 978 (TAAT)2=0.998 delTAAT=0.002
1000Genomes American Sub 694 (TAAT)2=1.000 delTAAT=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 (TAAT)2=0.9990 delTAAT=0.0010
UK 10K study - Twins TWIN COHORT Study-wide 3708 (TAAT)2=0.9987 delTAAT=0.0013

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 (TAAT)2= delTAAT
GRCh38.p13 chr 1 NC_000001.11:g.52153_52160= NC_000001.11:g.52153TAAT[1]
GRCh37.p13 chr 1 NC_000001.10:g.52153_52160= NC_000001.10:g.52153TAAT[1]

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#.

8 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1367645208 Aug 21, 2014 (142)
2 EVA_DECODE ss1584129265 Apr 01, 2015 (144)
3 EVA_UK10K_ALSPAC ss1700140307 Apr 01, 2015 (144)
4 EVA_UK10K_TWINSUK ss1700153025 Apr 01, 2015 (144)
5 GNOMAD ss2750603405 Nov 08, 2017 (151)
6 SWEGEN ss2986141844 Nov 08, 2017 (151)
7 TOPMED ss3066320025 Nov 08, 2017 (151)
8 EVA_DECODE ss3685990335 Jul 12, 2019 (153)
9 1000Genomes NC_000001.10 - 52153 Oct 11, 2018 (152)
10 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 52153 Oct 11, 2018 (152)
11 gnomAD - Genomes NC_000001.11 - 52153 Apr 25, 2021 (155)
12 UK 10K study - Twins NC_000001.10 - 52153 Oct 11, 2018 (152)
13 ALFA NC_000001.11 - 52153 Apr 25, 2021 (155)

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
ss1584129265 NC_000001.9:42015:TAAT: NC_000001.11:52152:TAATTAAT:TAAT (self)
169, 4, 4, ss1367645208, ss1700140307, ss1700153025, ss2750603405, ss2986141844 NC_000001.10:52152:TAAT: NC_000001.11:52152:TAATTAAT:TAAT (self)
3280, ss3066320025, ss3685990335 NC_000001.11:52152:TAAT: NC_000001.11:52152:TAATTAAT:TAAT (self)
967652976 NC_000001.11:52152:TAATTAAT:TAAT NC_000001.11:52152:TAATTAAT:TAAT

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs568235219


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