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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.

rs142753025

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:862155-862172 (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(AG)3A
Variation Type
Indel Insertion and Deletion
Frequency
delT(AG)3A=0.000156 (21/134882, GnomAD)
delT(AG)3A=0.01501 (178/11862, ALFA)
delT(AG)3A=0.0026 (10/3854, ALSPAC) (+ 1 more)
delT(AG)3A=0.0013 (5/3708, TWINSUK)
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.862157TAGAGAGA[1]
GRCh37.p13 chr 1 NC_000001.10:g.797537TAGAGAGA[1]
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 11862 GATAGAGAGATAGAGAGA=0.98499 GATAGAGAGA=0.01501
European Sub 7618 GATAGAGAGATAGAGAGA=0.9974 GATAGAGAGA=0.0026
African Sub 2816 GATAGAGAGATAGAGAGA=0.9741 GATAGAGAGA=0.0259
African Others Sub 108 GATAGAGAGATAGAGAGA=0.991 GATAGAGAGA=0.009
African American Sub 2708 GATAGAGAGATAGAGAGA=0.9734 GATAGAGAGA=0.0266
Asian Sub 108 GATAGAGAGATAGAGAGA=0.880 GATAGAGAGA=0.120
East Asian Sub 84 GATAGAGAGATAGAGAGA=0.87 GATAGAGAGA=0.13
Other Asian Sub 24 GATAGAGAGATAGAGAGA=0.92 GATAGAGAGA=0.08
Latin American 1 Sub 146 GATAGAGAGATAGAGAGA=0.952 GATAGAGAGA=0.048
Latin American 2 Sub 610 GATAGAGAGATAGAGAGA=0.926 GATAGAGAGA=0.074
South Asian Sub 94 GATAGAGAGATAGAGAGA=0.95 GATAGAGAGA=0.05
Other Sub 470 GATAGAGAGATAGAGAGA=0.968 GATAGAGAGA=0.032


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 134882 (GATAGAGA)2GA=0.999844 delT(AG)3A=0.000156
gnomAD - Genomes European Sub 75550 (GATAGAGA)2GA=1.00000 delT(AG)3A=0.00000
gnomAD - Genomes African Sub 39874 (GATAGAGA)2GA=0.99947 delT(AG)3A=0.00053
gnomAD - Genomes American Sub 12034 (GATAGAGA)2GA=1.00000 delT(AG)3A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3240 (GATAGAGA)2GA=1.0000 delT(AG)3A=0.0000
gnomAD - Genomes East Asian Sub 2166 (GATAGAGA)2GA=1.0000 delT(AG)3A=0.0000
gnomAD - Genomes Other Sub 2018 (GATAGAGA)2GA=1.0000 delT(AG)3A=0.0000
Allele Frequency Aggregator Total Global 11862 (GATAGAGA)2GA=0.98499 delT(AG)3A=0.01501
Allele Frequency Aggregator European Sub 7618 (GATAGAGA)2GA=0.9974 delT(AG)3A=0.0026
Allele Frequency Aggregator African Sub 2816 (GATAGAGA)2GA=0.9741 delT(AG)3A=0.0259
Allele Frequency Aggregator Latin American 2 Sub 610 (GATAGAGA)2GA=0.926 delT(AG)3A=0.074
Allele Frequency Aggregator Other Sub 470 (GATAGAGA)2GA=0.968 delT(AG)3A=0.032
Allele Frequency Aggregator Latin American 1 Sub 146 (GATAGAGA)2GA=0.952 delT(AG)3A=0.048
Allele Frequency Aggregator Asian Sub 108 (GATAGAGA)2GA=0.880 delT(AG)3A=0.120
Allele Frequency Aggregator South Asian Sub 94 (GATAGAGA)2GA=0.95 delT(AG)3A=0.05
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 (GATAGAGA)2GA=0.9974 delT(AG)3A=0.0026
UK 10K study - Twins TWIN COHORT Study-wide 3708 (GATAGAGA)2GA=0.9987 delT(AG)3A=0.0013
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 (GATAGAGA)2GA= delT(AG)3A
GRCh38.p13 chr 1 NC_000001.11:g.862155_862172= NC_000001.11:g.862157TAGAGAGA[1]
GRCh37.p13 chr 1 NC_000001.10:g.797535_797552= NC_000001.10:g.797537TAGAGAGA[1]
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, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 GMI ss287939326 May 04, 2012 (137)
2 1000GENOMES ss325997472 May 09, 2011 (134)
3 LUNTER ss552739005 Apr 25, 2013 (138)
4 EVA_UK10K_ALSPAC ss1700142688 Apr 01, 2015 (144)
5 EVA_UK10K_TWINSUK ss1700153574 Apr 01, 2015 (144)
6 GNOMAD ss2750641572 Nov 08, 2017 (151)
7 MCHAISSO ss3063573522 Nov 08, 2017 (151)
8 TOPMED ss3066405885 Nov 08, 2017 (151)
9 EVA_DECODE ss3685992487 Jul 12, 2019 (153)
10 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 797535 Oct 11, 2018 (152)
11 gnomAD - Genomes NC_000001.11 - 862155 Apr 25, 2021 (155)
12 UK 10K study - Twins NC_000001.10 - 797535 Oct 11, 2018 (152)
13 ALFA NC_000001.11 - 862155 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
ss287939326, ss325997472, ss552739005 NC_000001.9:787397:GATAGAGA: NC_000001.11:862154:GATAGAGAGATAGA…

NC_000001.11:862154:GATAGAGAGATAGAGAGA:GATAGAGAGA

(self)
510, 510, ss1700142688, ss1700153574, ss2750641572 NC_000001.10:797534:GATAGAGA: NC_000001.11:862154:GATAGAGAGATAGA…

NC_000001.11:862154:GATAGAGAGATAGAGAGA:GATAGAGAGA

(self)
71119, ss3063573522, ss3066405885, ss3685992487 NC_000001.11:862154:GATAGAGA: NC_000001.11:862154:GATAGAGAGATAGA…

NC_000001.11:862154:GATAGAGAGATAGAGAGA:GATAGAGAGA

(self)
31030707 NC_000001.11:862154:GATAGAGAGATAGA…

NC_000001.11:862154:GATAGAGAGATAGAGAGA:GATAGAGAGA

NC_000001.11:862154:GATAGAGAGATAGA…

NC_000001.11:862154:GATAGAGAGATAGAGAGA:GATAGAGAGA

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 rs142753025

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