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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.

rs200651397

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:72298-72301 (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
dupATT
Variation Type
Indel Insertion and Deletion
Frequency
dupATT=0.007787 (784/100686, GnomAD)
dupATT=0.04435 (731/16482, 8.3KJPN)
dupATT=0.00422 (50/11862, ALFA) (+ 2 more)
dupATT=0.0042 (21/5008, 1000G)
dupATT=0.0528 (96/1818, Korea1K)
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 1 NC_000001.11:g.72299_72301dup
GRCh37.p13 chr 1 NC_000001.10:g.72299_72301dup
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 11862 TATT=0.99578 TATTATT=0.00422
European Sub 7618 TATT=0.9997 TATTATT=0.0003
African Sub 2816 TATT=1.0000 TATTATT=0.0000
African Others Sub 108 TATT=1.000 TATTATT=0.000
African American Sub 2708 TATT=1.0000 TATTATT=0.0000
Asian Sub 108 TATT=0.917 TATTATT=0.083
East Asian Sub 84 TATT=0.93 TATTATT=0.07
Other Asian Sub 24 TATT=0.88 TATTATT=0.12
Latin American 1 Sub 146 TATT=1.000 TATTATT=0.000
Latin American 2 Sub 610 TATT=0.944 TATTATT=0.056
South Asian Sub 94 TATT=1.00 TATTATT=0.00
Other Sub 470 TATT=0.989 TATTATT=0.011


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 100686 -

No frequency provided

dupATT=0.007787
gnomAD - Genomes European Sub 48268 -

No frequency provided

dupATT=0.00029
gnomAD - Genomes African Sub 36032 -

No frequency provided

dupATT=0.00061
gnomAD - Genomes American Sub 9874 -

No frequency provided

dupATT=0.0607
gnomAD - Genomes East Asian Sub 3030 -

No frequency provided

dupATT=0.0413
gnomAD - Genomes Ashkenazi Jewish Sub 1990 -

No frequency provided

dupATT=0.0000
gnomAD - Genomes Other Sub 1492 -

No frequency provided

dupATT=0.0161
8.3KJPN JAPANESE Study-wide 16482 -

No frequency provided

dupATT=0.04435
Allele Frequency Aggregator Total Global 11862 TATT=0.99578 dupATT=0.00422
Allele Frequency Aggregator European Sub 7618 TATT=0.9997 dupATT=0.0003
Allele Frequency Aggregator African Sub 2816 TATT=1.0000 dupATT=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 TATT=0.944 dupATT=0.056
Allele Frequency Aggregator Other Sub 470 TATT=0.989 dupATT=0.011
Allele Frequency Aggregator Latin American 1 Sub 146 TATT=1.000 dupATT=0.000
Allele Frequency Aggregator Asian Sub 108 TATT=0.917 dupATT=0.083
Allele Frequency Aggregator South Asian Sub 94 TATT=1.00 dupATT=0.00
1000Genomes Global Study-wide 5008 -

No frequency provided

dupATT=0.0042
1000Genomes African Sub 1322 -

No frequency provided

dupATT=0.0000
1000Genomes East Asian Sub 1008 -

No frequency provided

dupATT=0.0109
1000Genomes Europe Sub 1006 -

No frequency provided

dupATT=0.0000
1000Genomes South Asian Sub 978 -

No frequency provided

dupATT=0.000
1000Genomes American Sub 694 -

No frequency provided

dupATT=0.014
Korean Genome Project KOREAN Study-wide 1818 -

No frequency provided

dupATT=0.0528
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 TATT= dupATT
GRCh38.p13 chr 1 NC_000001.11:g.72298_72301= NC_000001.11:g.72299_72301dup
GRCh37.p13 chr 1 NC_000001.10:g.72298_72301= NC_000001.10:g.72299_72301dup
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#.

9 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss498763762 May 04, 2012 (137)
2 SSMP ss663202774 Apr 01, 2015 (144)
3 1000GENOMES ss1367645224 Aug 21, 2014 (142)
4 GNOMAD ss2750605224 Nov 08, 2017 (151)
5 TOPMED ss3066324224 Nov 08, 2017 (151)
6 EVA_DECODE ss3685990529 Jul 12, 2019 (153)
7 KHV_HUMAN_GENOMES ss3798742517 Jul 12, 2019 (153)
8 KOGIC ss3943622817 Apr 25, 2020 (154)
9 TOMMO_GENOMICS ss5142033541 Apr 25, 2021 (155)
10 1000Genomes NC_000001.10 - 72298 Oct 11, 2018 (152)
11 gnomAD - Genomes NC_000001.11 - 72298 Apr 25, 2021 (155)
12 Korean Genome Project NC_000001.11 - 72298 Apr 25, 2020 (154)
13 8.3KJPN NC_000001.10 - 72298 Apr 25, 2021 (155)
14 ALFA NC_000001.11 - 72298 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
476, 2848, ss498763762, ss663202774, ss1367645224, ss2750605224, ss5142033541 NC_000001.10:72297::TAT NC_000001.11:72297:TATT:TATTATT (self)
6836, 818, ss3066324224, ss3685990529, ss3798742517, ss3943622817 NC_000001.11:72297::TAT NC_000001.11:72297:TATT:TATTATT (self)
350891013 NC_000001.11:72297:TATT:TATTATT NC_000001.11:72297:TATT:TATTATT
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 rs200651397

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