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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.

rs200769871

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:55250 (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
insATGGT
Variation Type
Indel Insertion and Deletion
Frequency
insATGGT=0.06236 (6133/98342, GnomAD)
insATGGT=0.27983 (4629/16542, 8.3KJPN)
insATGGT=0.00000 (0/10882, ALFA) (+ 6 more)
insATGGT=0.0070 (27/3854, ALSPAC)
insATGGT=0.0067 (25/3708, TWINSUK)
insATGGT=0.3018 (545/1806, Korea1K)
insATGGT=0.083 (40/484, NorthernSweden)
insATGGT=0.302 (64/212, Vietnamese)
insATGGT=0.06 (2/36, GENOME_DK)
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.55250_55251insATGGT
GRCh37.p13 chr 1 NC_000001.10:g.55250_55251insATGGT
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 10882 T=1.00000 TATGGT=0.00000
European Sub 7236 T=1.0000 TATGGT=0.0000
African Sub 2554 T=1.0000 TATGGT=0.0000
African Others Sub 100 T=1.00 TATGGT=0.00
African American Sub 2454 T=1.0000 TATGGT=0.0000
Asian Sub 46 T=1.00 TATGGT=0.00
East Asian Sub 34 T=1.00 TATGGT=0.00
Other Asian Sub 12 T=1.00 TATGGT=0.00
Latin American 1 Sub 138 T=1.000 TATGGT=0.000
Latin American 2 Sub 402 T=1.000 TATGGT=0.000
South Asian Sub 92 T=1.00 TATGGT=0.00
Other Sub 414 T=1.000 TATGGT=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 98342 -

No frequency provided

insATGGT=0.06236
gnomAD - Genomes European Sub 48098 -

No frequency provided

insATGGT=0.04154
gnomAD - Genomes African Sub 34568 -

No frequency provided

insATGGT=0.05245
gnomAD - Genomes American Sub 9330 -

No frequency provided

insATGGT=0.1370
gnomAD - Genomes East Asian Sub 2918 -

No frequency provided

insATGGT=0.2882
gnomAD - Genomes Ashkenazi Jewish Sub 1960 -

No frequency provided

insATGGT=0.0423
gnomAD - Genomes Other Sub 1468 -

No frequency provided

insATGGT=0.0817
8.3KJPN JAPANESE Study-wide 16542 -

No frequency provided

insATGGT=0.27983
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 -

No frequency provided

insATGGT=0.0070
UK 10K study - Twins TWIN COHORT Study-wide 3708 -

No frequency provided

insATGGT=0.0067
Korean Genome Project KOREAN Study-wide 1806 -

No frequency provided

insATGGT=0.3018
Northern Sweden ACPOP Study-wide 484 -

No frequency provided

insATGGT=0.083
A Vietnamese Genetic Variation Database Global Study-wide 212 -

No frequency provided

insATGGT=0.302
The Danish reference pan genome Danish Study-wide 36 -

No frequency provided

insATGGT=0.06
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= insATGGT
GRCh38.p13 chr 1 NC_000001.11:g.55250= NC_000001.11:g.55250_55251insATGGT
GRCh37.p13 chr 1 NC_000001.10:g.55250= NC_000001.10:g.55250_55251insATGGT
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#.

17 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss498763759 May 04, 2012 (137)
2 LUNTER ss550899107 Apr 25, 2013 (138)
3 LUNTER ss550899108 Apr 25, 2013 (138)
4 LUNTER ss552738957 Apr 25, 2013 (138)
5 SSMP ss663193528 Apr 01, 2015 (144)
6 EVA_GENOME_DK ss1573866955 Apr 01, 2015 (144)
7 EVA_UK10K_ALSPAC ss1700140357 Apr 01, 2015 (144)
8 EVA_UK10K_TWINSUK ss1700153055 Apr 01, 2015 (144)
9 JJLAB ss2030297671 Sep 14, 2016 (149)
10 GNOMAD ss2750603661 Nov 08, 2017 (151)
11 SWEGEN ss2986141908 Nov 08, 2017 (151)
12 TOPMED ss3066320682 Nov 08, 2017 (151)
13 EVA_DECODE ss3685990384 Jul 12, 2019 (153)
14 ACPOP ss3726715180 Jul 12, 2019 (153)
15 EVA ss3825981325 Apr 25, 2020 (154)
16 KOGIC ss3943622538 Apr 25, 2020 (154)
17 TOMMO_GENOMICS ss5142032630 Apr 25, 2021 (155)
18 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 55250 Oct 11, 2018 (152)
19 The Danish reference pan genome NC_000001.10 - 55250 Apr 25, 2020 (154)
20 gnomAD - Genomes NC_000001.11 - 55250 Apr 25, 2021 (155)
21 Korean Genome Project NC_000001.11 - 55250 Apr 25, 2020 (154)
22 Northern Sweden NC_000001.10 - 55250 Jul 12, 2019 (153)
23 8.3KJPN NC_000001.10 - 55250 Apr 25, 2021 (155)
24 UK 10K study - Twins NC_000001.10 - 55250 Oct 11, 2018 (152)
25 A Vietnamese Genetic Variation Database NC_000001.10 - 55250 Jul 12, 2019 (153)
26 ALFA NC_000001.11 - 55250 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
ss550899107, ss550899108, ss552738957 NC_000001.9:45112::TATGG NC_000001.11:55249:T:TATGGT (self)
15, 120129, 45, 1937, 15, 1, ss498763759, ss663193528, ss1573866955, ss1700140357, ss1700153055, ss2030297671, ss2750603661, ss2986141908, ss3726715180, ss3825981325, ss5142032630 NC_000001.10:55249::TATGG NC_000001.11:55249:T:TATGGT (self)
3930, 539, ss3066320682, ss3685990384, ss3943622538 NC_000001.11:55249::TATGG NC_000001.11:55249:T:TATGGT (self)
7327884661 NC_000001.11:55249:T:TATGGT NC_000001.11:55249:T:TATGGT
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 rs200769871

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