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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.

rs149025072

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:861997-862003 (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
delAGAT / dupAGAT
Variation Type
Indel Insertion and Deletion
Frequency
delAGAT=0.11319 (1897/16760, 8.3KJPN)
delAGAT=0.02518 (365/14494, ALFA)
delAGAT=0.1108 (203/1832, Korea1K) (+ 1 more)
delAGAT=0.088 (53/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC107984850 : Intron Variant
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.862000_862003del
GRCh38.p13 chr 1 NC_000001.11:g.862000_862003dup
GRCh37.p13 chr 1 NC_000001.10:g.797380_797383del
GRCh37.p13 chr 1 NC_000001.10:g.797380_797383dup
Gene: LOC107984850, uncharacterized LOC107984850 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107984850 transcript variant X1 XR_001737607.2:n. N/A Intron Variant
LOC107984850 transcript variant X2 XR_001737608.2:n. N/A Intron Variant
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 14494 GATAGAT=0.97482 GAT=0.02518, GATAGATAGAT=0.00000
European Sub 10740 GATAGAT=0.96601 GAT=0.03399, GATAGATAGAT=0.00000
African Sub 2498 GATAGAT=1.0000 GAT=0.0000, GATAGATAGAT=0.0000
African Others Sub 102 GATAGAT=1.000 GAT=0.000, GATAGATAGAT=0.000
African American Sub 2396 GATAGAT=1.0000 GAT=0.0000, GATAGATAGAT=0.0000
Asian Sub 96 GATAGAT=1.00 GAT=0.00, GATAGATAGAT=0.00
East Asian Sub 76 GATAGAT=1.00 GAT=0.00, GATAGATAGAT=0.00
Other Asian Sub 20 GATAGAT=1.00 GAT=0.00, GATAGATAGAT=0.00
Latin American 1 Sub 130 GATAGAT=1.000 GAT=0.000, GATAGATAGAT=0.000
Latin American 2 Sub 548 GATAGAT=1.000 GAT=0.000, GATAGATAGAT=0.000
South Asian Sub 72 GATAGAT=1.00 GAT=0.00, GATAGATAGAT=0.00
Other Sub 410 GATAGAT=1.000 GAT=0.000, GATAGATAGAT=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
8.3KJPN JAPANESE Study-wide 16760 GATAGAT=0.88681 delAGAT=0.11319
Korean Genome Project KOREAN Study-wide 1832 GATAGAT=0.8892 delAGAT=0.1108
Northern Sweden ACPOP Study-wide 600 GATAGAT=0.912 delAGAT=0.088
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 GATAGAT= delAGAT dupAGAT
GRCh38.p13 chr 1 NC_000001.11:g.861997_862003= NC_000001.11:g.862000_862003del NC_000001.11:g.862000_862003dup
GRCh37.p13 chr 1 NC_000001.10:g.797377_797383= NC_000001.10:g.797380_797383del NC_000001.10:g.797380_797383dup
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#.

15 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss325997469 May 09, 2011 (134)
2 LUNTER ss550899139 Apr 25, 2013 (138)
3 LUNTER ss550903132 Apr 25, 2013 (138)
4 LUNTER ss552739003 Apr 25, 2013 (138)
5 SSMP ss663206834 Apr 01, 2015 (144)
6 DDI ss1536213894 Apr 01, 2015 (144)
7 GNOMAD ss2750641551 Nov 08, 2017 (151)
8 SWEGEN ss2986149468 Nov 08, 2017 (151)
9 TOPMED ss3066405844 Nov 08, 2017 (151)
10 TOPMED ss3066405845 Nov 08, 2017 (151)
11 EVA_DECODE ss3685992484 Jul 12, 2019 (153)
12 ACPOP ss3726716516 Jul 12, 2019 (153)
13 KOGIC ss3943630086 Apr 25, 2020 (154)
14 GNOMAD ss3986930743 Apr 25, 2021 (155)
15 TOMMO_GENOMICS ss5142053283 Apr 25, 2021 (155)
16 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 71083 (NC_000001.11:861996::GATA 1/132248)
Row 71084 (NC_000001.11:861996:GATA: 10089/125310)

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

Submission ignored due to conflicting rows:
Row 71083 (NC_000001.11:861996::GATA 1/132248)
Row 71084 (NC_000001.11:861996:GATA: 10089/125310)

- Apr 25, 2021 (155)
18 Korean Genome Project NC_000001.11 - 861997 Apr 25, 2020 (154)
19 Northern Sweden NC_000001.10 - 797377 Jul 12, 2019 (153)
20 8.3KJPN NC_000001.10 - 797377 Apr 25, 2021 (155)
21 ALFA NC_000001.11 - 861997 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
ss325997469, ss550899139, ss550903132, ss552739003 NC_000001.9:787239:GATA: NC_000001.11:861996:GATAGAT:GAT (self)
1381, 22590, ss663206834, ss2750641551, ss2986149468, ss3726716516, ss5142053283 NC_000001.10:797376:GATA: NC_000001.11:861996:GATAGAT:GAT (self)
8087, ss3066405845, ss3943630086 NC_000001.11:861996:GATA: NC_000001.11:861996:GATAGAT:GAT (self)
6065790444 NC_000001.11:861996:GATAGAT:GAT NC_000001.11:861996:GATAGAT:GAT
ss3685992484 NC_000001.11:861999:AGAT: NC_000001.11:861996:GATAGAT:GAT (self)
ss1536213894 NC_000001.10:797376::GATA NC_000001.11:861996:GATAGAT:GATAGA…

NC_000001.11:861996:GATAGAT:GATAGATAGAT

(self)
ss3066405844, ss3986930743 NC_000001.11:861996::GATA NC_000001.11:861996:GATAGAT:GATAGA…

NC_000001.11:861996:GATAGAT:GATAGATAGAT

(self)
6065790444 NC_000001.11:861996:GATAGAT:GATAGA…

NC_000001.11:861996:GATAGAT:GATAGATAGAT

NC_000001.11:861996:GATAGAT:GATAGA…

NC_000001.11:861996:GATAGAT:GATAGATAGAT

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 rs149025072

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