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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.

rs200079338

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:279525-279534 (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
delT / dupT / dupTT / dupTTT
Variation Type
Indel Insertion and Deletion
Frequency
dupTTT=0.000008 (2/264690, TOPMED)
dupT=0.05168 (811/15692, ALFA)
dupT=0.27605 (4170/15106, 8.3KJPN) (+ 1 more)
dupT=0.1024 (513/5008, 1000G)
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.279534del
GRCh38.p13 chr 1 NC_000001.11:g.279534dup
GRCh38.p13 chr 1 NC_000001.11:g.279533_279534dup
GRCh38.p13 chr 1 NC_000001.11:g.279532_279534dup
GRCh37.p13 chr 1 NC_000001.10:g.249285del
GRCh37.p13 chr 1 NC_000001.10:g.249285dup
GRCh37.p13 chr 1 NC_000001.10:g.249284_249285dup
GRCh37.p13 chr 1 NC_000001.10:g.249283_249285dup
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 15692 TTTTTTTTTT=0.94832 TTTTTTTTT=0.00000, TTTTTTTTTTT=0.05168, TTTTTTTTTTTT=0.00000, TTTTTTTTTTTTT=0.00000
European Sub 11922 TTTTTTTTTT=0.93223 TTTTTTTTT=0.00000, TTTTTTTTTTT=0.06777, TTTTTTTTTTTT=0.00000, TTTTTTTTTTTTT=0.00000
African Sub 2556 TTTTTTTTTT=1.0000 TTTTTTTTT=0.0000, TTTTTTTTTTT=0.0000, TTTTTTTTTTTT=0.0000, TTTTTTTTTTTTT=0.0000
African Others Sub 106 TTTTTTTTTT=1.000 TTTTTTTTT=0.000, TTTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000, TTTTTTTTTTTTT=0.000
African American Sub 2450 TTTTTTTTTT=1.0000 TTTTTTTTT=0.0000, TTTTTTTTTTT=0.0000, TTTTTTTTTTTT=0.0000, TTTTTTTTTTTTT=0.0000
Asian Sub 72 TTTTTTTTTT=1.00 TTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00, TTTTTTTTTTTTT=0.00
East Asian Sub 52 TTTTTTTTTT=1.00 TTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00, TTTTTTTTTTTTT=0.00
Other Asian Sub 20 TTTTTTTTTT=1.00 TTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00, TTTTTTTTTTTTT=0.00
Latin American 1 Sub 126 TTTTTTTTTT=1.000 TTTTTTTTT=0.000, TTTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000, TTTTTTTTTTTTT=0.000
Latin American 2 Sub 506 TTTTTTTTTT=1.000 TTTTTTTTT=0.000, TTTTTTTTTTT=0.000, TTTTTTTTTTTT=0.000, TTTTTTTTTTTTT=0.000
South Asian Sub 82 TTTTTTTTTT=1.00 TTTTTTTTT=0.00, TTTTTTTTTTT=0.00, TTTTTTTTTTTT=0.00, TTTTTTTTTTTTT=0.00
Other Sub 428 TTTTTTTTTT=0.993 TTTTTTTTT=0.000, TTTTTTTTTTT=0.007, TTTTTTTTTTTT=0.000, TTTTTTTTTTTTT=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
TopMed Global Study-wide 264690 -

No frequency provided

dupTTT=0.000008
8.3KJPN JAPANESE Study-wide 15106 -

No frequency provided

dupT=0.27605
1000Genomes Global Study-wide 5008 -

No frequency provided

dupT=0.1024
1000Genomes African Sub 1322 -

No frequency provided

dupT=0.0333
1000Genomes East Asian Sub 1008 -

No frequency provided

dupT=0.2143
1000Genomes Europe Sub 1006 -

No frequency provided

dupT=0.1143
1000Genomes South Asian Sub 978 -

No frequency provided

dupT=0.100
1000Genomes American Sub 694 -

No frequency provided

dupT=0.058
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 (T)10= delT dupT dupTT dupTTT
GRCh38.p13 chr 1 NC_000001.11:g.279525_279534= NC_000001.11:g.279534del NC_000001.11:g.279534dup NC_000001.11:g.279533_279534dup NC_000001.11:g.279532_279534dup
GRCh37.p13 chr 1 NC_000001.10:g.249276_249285= NC_000001.10:g.249285del NC_000001.10:g.249285dup NC_000001.10:g.249284_249285dup NC_000001.10:g.249283_249285dup
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#.

22 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 GMI ss287939222 May 04, 2012 (137)
2 1000GENOMES ss498763776 May 04, 2012 (138)
3 LUNTER ss550903091 Apr 25, 2013 (138)
4 1000GENOMES ss1367645246 Aug 21, 2014 (142)
5 SWEGEN ss2986144351 Nov 08, 2017 (151)
6 MCHAISSO ss3063573445 Nov 08, 2017 (151)
7 MCHAISSO ss3064385961 Nov 08, 2017 (151)
8 MCHAISSO ss3065282436 Nov 08, 2017 (151)
9 TOPMED ss3066350287 Nov 08, 2017 (151)
10 TOPMED ss3066350288 Nov 08, 2017 (151)
11 TOPMED ss3066350289 Nov 08, 2017 (151)
12 TOPMED ss3066350291 Nov 08, 2017 (151)
13 EVA_DECODE ss3685991075 Jul 12, 2019 (153)
14 PACBIO ss3783301717 Jul 12, 2019 (153)
15 KHV_HUMAN_GENOMES ss3798742678 Jul 12, 2019 (153)
16 KOGIC ss3943625112 Apr 25, 2020 (154)
17 KOGIC ss3943625113 Apr 25, 2020 (154)
18 GNOMAD ss3986906099 Apr 25, 2021 (155)
19 GNOMAD ss3986906100 Apr 25, 2021 (155)
20 GNOMAD ss3986906101 Apr 25, 2021 (155)
21 TOPMED ss4436405959 Apr 25, 2021 (155)
22 TOMMO_GENOMICS ss5142040197 Apr 25, 2021 (155)
23 1000Genomes NC_000001.10 - 249276 Oct 11, 2018 (152)
24 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 27547 (NC_000001.11:279524::T 18176/125632)
Row 27548 (NC_000001.11:279524::TT 17/126028)
Row 27549 (NC_000001.11:279524::TTT 2/126034)

- Apr 25, 2021 (155)
25 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 27547 (NC_000001.11:279524::T 18176/125632)
Row 27548 (NC_000001.11:279524::TT 17/126028)
Row 27549 (NC_000001.11:279524::TTT 2/126034)

- Apr 25, 2021 (155)
26 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 27547 (NC_000001.11:279524::T 18176/125632)
Row 27548 (NC_000001.11:279524::TT 17/126028)
Row 27549 (NC_000001.11:279524::TTT 2/126034)

- Apr 25, 2021 (155)
27 Korean Genome Project

Submission ignored due to conflicting rows:
Row 3113 (NC_000001.11:279524::T 512/1598)
Row 3114 (NC_000001.11:279524::TT 3/1598)

- Apr 25, 2020 (154)
28 Korean Genome Project

Submission ignored due to conflicting rows:
Row 3113 (NC_000001.11:279524::T 512/1598)
Row 3114 (NC_000001.11:279524::TT 3/1598)

- Apr 25, 2020 (154)
29 8.3KJPN NC_000001.10 - 249276 Apr 25, 2021 (155)
30 TopMed NC_000001.11 - 279525 Apr 25, 2021 (155)
31 ALFA NC_000001.11 - 279525 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).

Associated ID History Updated (Build)
rs200176617 May 15, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3783301717 NC_000001.10:249275:T: NC_000001.11:279524:TTTTTTTTTT:TTT…

NC_000001.11:279524:TTTTTTTTTT:TTTTTTTTT

(self)
ss3066350291 NC_000001.11:279524:T: NC_000001.11:279524:TTTTTTTTTT:TTT…

NC_000001.11:279524:TTTTTTTTTT:TTTTTTTTT

(self)
3284777637 NC_000001.11:279524:TTTTTTTTTT:TTT…

NC_000001.11:279524:TTTTTTTTTT:TTTTTTTTT

NC_000001.11:279524:TTTTTTTTTT:TTT…

NC_000001.11:279524:TTTTTTTTTT:TTTTTTTTT

ss550903091 NC_000001.9:239138::T NC_000001.11:279524:TTTTTTTTTT:TTT…

NC_000001.11:279524:TTTTTTTTTT:TTTTTTTTTTT

(self)
ss287939222 NC_000001.9:239148::T NC_000001.11:279524:TTTTTTTTTT:TTT…

NC_000001.11:279524:TTTTTTTTTT:TTTTTTTTTTT

(self)
1145, 9504, ss498763776, ss1367645246, ss2986144351, ss5142040197 NC_000001.10:249275::T NC_000001.11:279524:TTTTTTTTTT:TTT…

NC_000001.11:279524:TTTTTTTTTT:TTTTTTTTTTT

(self)
ss3063573445, ss3064385961, ss3065282436, ss3066350287, ss3685991075, ss3798742678, ss3943625112, ss3986906099 NC_000001.11:279524::T NC_000001.11:279524:TTTTTTTTTT:TTT…

NC_000001.11:279524:TTTTTTTTTT:TTTTTTTTTTT

(self)
3284777637 NC_000001.11:279524:TTTTTTTTTT:TTT…

NC_000001.11:279524:TTTTTTTTTT:TTTTTTTTTTT

NC_000001.11:279524:TTTTTTTTTT:TTT…

NC_000001.11:279524:TTTTTTTTTT:TTTTTTTTTTT

ss3066350288, ss3943625113, ss3986906100 NC_000001.11:279524::TT NC_000001.11:279524:TTTTTTTTTT:TTT…

NC_000001.11:279524:TTTTTTTTTT:TTTTTTTTTTTT

(self)
3284777637 NC_000001.11:279524:TTTTTTTTTT:TTT…

NC_000001.11:279524:TTTTTTTTTT:TTTTTTTTTTTT

NC_000001.11:279524:TTTTTTTTTT:TTT…

NC_000001.11:279524:TTTTTTTTTT:TTTTTTTTTTTT

3308, 12294, ss3066350289, ss3986906101, ss4436405959 NC_000001.11:279524::TTT NC_000001.11:279524:TTTTTTTTTT:TTT…

NC_000001.11:279524:TTTTTTTTTT:TTTTTTTTTTTTT

(self)
3284777637 NC_000001.11:279524:TTTTTTTTTT:TTT…

NC_000001.11:279524:TTTTTTTTTT:TTTTTTTTTTTTT

NC_000001.11:279524:TTTTTTTTTT:TTT…

NC_000001.11:279524:TTTTTTTTTT:TTTTTTTTTTTTT

(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 rs200079338

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