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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.

rs112791300

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:902174-902180 (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
delTGTG
Variation Type
Indel Insertion and Deletion
Frequency
delTGTG=0.033496 (8866/264690, TOPMED)
delTGTG=0.034492 (4836/140206, GnomAD)
delTGTG=0.02824 (523/18520, ALFA) (+ 10 more)
delTGTG=0.11760 (1971/16760, 8.3KJPN)
delTGTG=0.0387 (194/5008, 1000G)
delTGTG=0.0181 (81/4480, Estonian)
delTGTG=0.0192 (74/3854, ALSPAC)
delTGTG=0.0178 (66/3708, TWINSUK)
delTGTG=0.0393 (72/1832, Korea1K)
delTGTG=0.016 (16/998, GoNL)
delTGTG=0.010 (6/600, NorthernSweden)
delTGTG=0.019 (4/210, Vietnamese)
delTGTG=0.07 (3/40, 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.902175TG[1]
GRCh37.p13 chr 1 NC_000001.10:g.837555TG[1]
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 18520 GTGTGTG=0.97176 GTG=0.02824
European Sub 14152 GTGTGTG=0.97901 GTG=0.02099
African Sub 2898 GTGTGTG=0.9337 GTG=0.0663
African Others Sub 114 GTGTGTG=0.930 GTG=0.070
African American Sub 2784 GTGTGTG=0.9339 GTG=0.0661
Asian Sub 112 GTGTGTG=0.982 GTG=0.018
East Asian Sub 86 GTGTGTG=0.98 GTG=0.02
Other Asian Sub 26 GTGTGTG=1.00 GTG=0.00
Latin American 1 Sub 146 GTGTGTG=0.966 GTG=0.034
Latin American 2 Sub 610 GTGTGTG=0.990 GTG=0.010
South Asian Sub 98 GTGTGTG=1.00 GTG=0.00
Other Sub 504 GTGTGTG=0.958 GTG=0.042


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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 (GT)3G=0.966504 delTGTG=0.033496
gnomAD - Genomes Global Study-wide 140206 (GT)3G=0.965508 delTGTG=0.034492
gnomAD - Genomes European Sub 75928 (GT)3G=0.97565 delTGTG=0.02435
gnomAD - Genomes African Sub 42016 (GT)3G=0.94107 delTGTG=0.05893
gnomAD - Genomes American Sub 13660 (GT)3G=0.98133 delTGTG=0.01867
gnomAD - Genomes Ashkenazi Jewish Sub 3322 (GT)3G=0.9690 delTGTG=0.0310
gnomAD - Genomes East Asian Sub 3132 (GT)3G=0.9757 delTGTG=0.0243
gnomAD - Genomes Other Sub 2148 (GT)3G=0.9642 delTGTG=0.0358
8.3KJPN JAPANESE Study-wide 16760 (GT)3G=0.88240 delTGTG=0.11760
1000Genomes Global Study-wide 5008 (GT)3G=0.9613 delTGTG=0.0387
1000Genomes African Sub 1322 (GT)3G=0.9221 delTGTG=0.0779
1000Genomes East Asian Sub 1008 (GT)3G=0.9524 delTGTG=0.0476
1000Genomes Europe Sub 1006 (GT)3G=0.9781 delTGTG=0.0219
1000Genomes South Asian Sub 978 (GT)3G=0.991 delTGTG=0.009
1000Genomes American Sub 694 (GT)3G=0.983 delTGTG=0.017
Genetic variation in the Estonian population Estonian Study-wide 4480 (GT)3G=0.9819 delTGTG=0.0181
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 (GT)3G=0.9808 delTGTG=0.0192
UK 10K study - Twins TWIN COHORT Study-wide 3708 (GT)3G=0.9822 delTGTG=0.0178
Korean Genome Project KOREAN Study-wide 1832 (GT)3G=0.9607 delTGTG=0.0393
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 (GT)3G=0.984 delTGTG=0.016
Northern Sweden ACPOP Study-wide 600 (GT)3G=0.990 delTGTG=0.010
A Vietnamese Genetic Variation Database Global Study-wide 210 (GT)3G=0.981 delTGTG=0.019
The Danish reference pan genome Danish Study-wide 40 (GT)3G=0.93 delTGTG=0.07
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 (GT)3G= delTGTG
GRCh38.p13 chr 1 NC_000001.11:g.902174_902180= NC_000001.11:g.902175TG[1]
GRCh37.p13 chr 1 NC_000001.10:g.837554_837560= NC_000001.10:g.837555TG[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#.

24 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss325997513 May 09, 2011 (135)
2 1000GENOMES ss498763865 May 04, 2012 (137)
3 LUNTER ss550899154 Apr 25, 2013 (138)
4 LUNTER ss552739030 Apr 25, 2013 (138)
5 TISHKOFF ss553708539 Apr 25, 2013 (138)
6 SSMP ss663209652 Apr 01, 2015 (144)
7 EVA-GONL ss974769902 Aug 21, 2014 (142)
8 1000GENOMES ss1367645477 Aug 21, 2014 (142)
9 EVA_GENOME_DK ss1573868307 Apr 01, 2015 (144)
10 EVA_DECODE ss1584129821 Apr 01, 2015 (144)
11 EVA_UK10K_ALSPAC ss1700143221 Apr 01, 2015 (144)
12 EVA_UK10K_TWINSUK ss1700153776 Apr 01, 2015 (144)
13 JJLAB ss2030297761 Sep 14, 2016 (149)
14 TOPMED ss2321507198 Dec 20, 2016 (150)
15 GNOMAD ss2750646080 Nov 08, 2017 (151)
16 SWEGEN ss2986150614 Nov 08, 2017 (151)
17 TOPMED ss3066413870 Nov 08, 2017 (151)
18 EGCUT_WGS ss3654261819 Jul 12, 2019 (153)
19 EVA_DECODE ss3685993034 Jul 12, 2019 (153)
20 ACPOP ss3726716751 Jul 12, 2019 (153)
21 KHV_HUMAN_GENOMES ss3798744243 Jul 12, 2019 (153)
22 KOGIC ss3943630892 Apr 25, 2020 (154)
23 TOPMED ss4436448656 Apr 25, 2021 (155)
24 TOMMO_GENOMICS ss5142055389 Apr 25, 2021 (155)
25 1000Genomes NC_000001.10 - 837554 Oct 11, 2018 (152)
26 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 837554 Oct 11, 2018 (152)
27 Genetic variation in the Estonian population NC_000001.10 - 837554 Oct 11, 2018 (152)
28 The Danish reference pan genome NC_000001.10 - 837554 Apr 25, 2020 (154)
29 gnomAD - Genomes NC_000001.11 - 902174 Apr 25, 2021 (155)
30 Genome of the Netherlands Release 5 NC_000001.10 - 837554 Apr 25, 2020 (154)
31 Korean Genome Project NC_000001.11 - 902174 Apr 25, 2020 (154)
32 Northern Sweden NC_000001.10 - 837554 Jul 12, 2019 (153)
33 8.3KJPN NC_000001.10 - 837554 Apr 25, 2021 (155)
34 TopMed NC_000001.11 - 902174 Apr 25, 2021 (155)
35 UK 10K study - Twins NC_000001.10 - 837554 Oct 11, 2018 (152)
36 A Vietnamese Genetic Variation Database NC_000001.10 - 837554 Jul 12, 2019 (153)
37 ALFA NC_000001.11 - 902174 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)
rs145176156 Sep 17, 2011 (135)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss325997513, ss550899154, ss552739030, ss1584129821 NC_000001.9:827416:GTGT: NC_000001.11:902173:GTGTGTG:GTG (self)
6195, 891, 67, 120267, 870, 1616, 24696, 891, 188, ss498763865, ss663209652, ss974769902, ss1367645477, ss1573868307, ss1700143221, ss1700153776, ss2030297761, ss2321507198, ss2750646080, ss2986150614, ss3654261819, ss3726716751, ss5142055389 NC_000001.10:837553:GTGT: NC_000001.11:902173:GTGTGTG:GTG (self)
ss553708539 NC_000001.10:837556:TGTG: NC_000001.11:902173:GTGTGTG:GTG (self)
78994, 8893, 26539, 54991, ss3066413870, ss3685993034, ss3798744243, ss3943630892, ss4436448656 NC_000001.11:902173:GTGT: NC_000001.11:902173:GTGTGTG:GTG (self)
8216246035 NC_000001.11:902173:GTGTGTG:GTG NC_000001.11:902173:GTGTGTG:GTG (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 rs112791300

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