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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.

rs34017275

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:896918-896919 (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
delTG
Variation Type
Deletion
Frequency
TG=0.355495 (94096/264690, TOPMED)
TG=0.368692 (51524/139748, GnomAD)
TG=0.34800 (6445/18520, ALFA) (+ 8 more)
TG=0.28300 (4743/16760, 8.3KJPN)
TG=0.3357 (1681/5008, 1000G)
TG=0.2883 (1111/3854, ALSPAC)
TG=0.2856 (1059/3708, TWINSUK)
TG=0.1556 (285/1832, Korea1K)
TG=0.328 (197/600, NorthernSweden)
TG=0.203 (43/212, Vietnamese)
TG=0.35 (14/40, 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.896918_896919del
GRCh37.p13 chr 1 NC_000001.10:g.832298_832299del
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 TG=0.34800 =0.65200
European Sub 14152 TG=0.31805 =0.68195
African Sub 2898 TG=0.5128 =0.4872
African Others Sub 114 TG=0.535 =0.465
African American Sub 2784 TG=0.5119 =0.4881
Asian Sub 112 TG=0.143 =0.857
East Asian Sub 86 TG=0.13 =0.87
Other Asian Sub 26 TG=0.19 =0.81
Latin American 1 Sub 146 TG=0.377 =0.623
Latin American 2 Sub 610 TG=0.293 =0.707
South Asian Sub 98 TG=0.22 =0.78
Other Sub 504 TG=0.369 =0.631


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 TG=0.355495 delTG=0.644505
gnomAD - Genomes Global Study-wide 139748 TG=0.368692 delTG=0.631308
gnomAD - Genomes European Sub 75672 TG=0.30994 delTG=0.69006
gnomAD - Genomes African Sub 41862 TG=0.51806 delTG=0.48194
gnomAD - Genomes American Sub 13618 TG=0.30687 delTG=0.69313
gnomAD - Genomes Ashkenazi Jewish Sub 3320 TG=0.3133 delTG=0.6867
gnomAD - Genomes East Asian Sub 3124 TG=0.1348 delTG=0.8652
gnomAD - Genomes Other Sub 2152 TG=0.3453 delTG=0.6547
8.3KJPN JAPANESE Study-wide 16760 TG=0.28300 delTG=0.71700
1000Genomes Global Study-wide 5008 TG=0.3357 delTG=0.6643
1000Genomes African Sub 1322 TG=0.5552 delTG=0.4448
1000Genomes East Asian Sub 1008 TG=0.1905 delTG=0.8095
1000Genomes Europe Sub 1006 TG=0.2962 delTG=0.7038
1000Genomes South Asian Sub 978 TG=0.247 delTG=0.753
1000Genomes American Sub 694 TG=0.310 delTG=0.690
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 TG=0.2883 delTG=0.7117
UK 10K study - Twins TWIN COHORT Study-wide 3708 TG=0.2856 delTG=0.7144
Korean Genome Project KOREAN Study-wide 1832 TG=0.1556 delTG=0.8444
Northern Sweden ACPOP Study-wide 600 TG=0.328 delTG=0.672
A Vietnamese Genetic Variation Database Global Study-wide 212 TG=0.203 delTG=0.797
The Danish reference pan genome Danish Study-wide 40 TG=0.35 delTG=0.65
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 TG= delTG
GRCh38.p13 chr 1 NC_000001.11:g.896918_896919= NC_000001.11:g.896918_896919del
GRCh37.p13 chr 1 NC_000001.10:g.832298_832299= NC_000001.10:g.832298_832299del
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#.

45 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 ABI ss41278923 Mar 13, 2006 (126)
2 HGSV ss79869646 Dec 15, 2007 (130)
3 HGSV ss79976729 Dec 15, 2007 (130)
4 HGSV ss80040305 Dec 15, 2007 (130)
5 HUMANGENOME_JCVI ss95218905 Feb 05, 2009 (130)
6 BCMHGSC_JDW ss103475671 Dec 01, 2009 (131)
7 GMI ss229263669 May 09, 2011 (134)
8 BL ss255892657 May 09, 2011 (135)
9 GMI ss287939384 May 04, 2012 (137)
10 PJP ss294562339 May 09, 2011 (135)
11 1000GENOMES ss325997504 May 09, 2011 (135)
12 1000GENOMES ss498763860 May 04, 2012 (137)
13 LUNTER ss550899148 Apr 25, 2013 (138)
14 LUNTER ss550903136 Apr 25, 2013 (138)
15 LUNTER ss552739023 Apr 25, 2013 (138)
16 SSMP ss663209354 Apr 01, 2015 (144)
17 BILGI_BIOE ss666080088 Apr 25, 2013 (138)
18 1000GENOMES ss1367645468 Aug 21, 2014 (142)
19 EVA_GENOME_DK ss1573868295 Apr 01, 2015 (144)
20 EVA_DECODE ss1584129761 Apr 01, 2015 (144)
21 EVA_UK10K_ALSPAC ss1700143187 Apr 01, 2015 (144)
22 EVA_UK10K_TWINSUK ss1700153739 Apr 01, 2015 (144)
23 HAMMER_LAB ss1793709389 Sep 08, 2015 (146)
24 JJLAB ss2030297756 Sep 14, 2016 (149)
25 TOPMED ss2321506829 Dec 20, 2016 (150)
26 SYSTEMSBIOZJU ss2624264890 Nov 08, 2017 (151)
27 GNOMAD ss2750645575 Nov 08, 2017 (151)
28 SWEGEN ss2986150524 Nov 08, 2017 (151)
29 MCHAISSO ss3063573539 Nov 08, 2017 (151)
30 MCHAISSO ss3064386050 Nov 08, 2017 (151)
31 TOPMED ss3066412844 Nov 08, 2017 (151)
32 BEROUKHIMLAB ss3644051501 Oct 11, 2018 (152)
33 URBANLAB ss3646581343 Oct 11, 2018 (152)
34 EVA_DECODE ss3685992932 Jul 12, 2019 (153)
35 ACPOP ss3726716689 Jul 12, 2019 (153)
36 PACBIO ss3783302473 Jul 12, 2019 (153)
37 PACBIO ss3788980136 Jul 12, 2019 (153)
38 PACBIO ss3793852696 Jul 12, 2019 (153)
39 KHV_HUMAN_GENOMES ss3798744173 Jul 12, 2019 (153)
40 EVA ss3825981596 Apr 25, 2020 (154)
41 EVA ss3836378521 Apr 25, 2020 (154)
42 EVA ss3841782535 Apr 25, 2020 (154)
43 KOGIC ss3943630787 Apr 25, 2020 (154)
44 TOPMED ss4436447235 Apr 25, 2021 (155)
45 TOMMO_GENOMICS ss5142055167 Apr 25, 2021 (155)
46 1000Genomes NC_000001.10 - 832298 Oct 11, 2018 (152)
47 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 832298 Oct 11, 2018 (152)
48 The Danish reference pan genome NC_000001.10 - 832298 Apr 25, 2020 (154)
49 gnomAD - Genomes NC_000001.11 - 896918 Apr 25, 2021 (155)
50 Korean Genome Project NC_000001.11 - 896918 Apr 25, 2020 (154)
51 Northern Sweden NC_000001.10 - 832298 Jul 12, 2019 (153)
52 8.3KJPN NC_000001.10 - 832298 Apr 25, 2021 (155)
53 TopMed NC_000001.11 - 896918 Apr 25, 2021 (155)
54 UK 10K study - Twins NC_000001.10 - 832298 Oct 11, 2018 (152)
55 A Vietnamese Genetic Variation Database NC_000001.10 - 832298 Jul 12, 2019 (153)
56 ALFA NC_000001.11 - 896918 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)
rs58644096 May 24, 2008 (130)
rs138126878 Sep 17, 2011 (135)
rs143202331 Sep 17, 2011 (135)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss79869646, ss79976729, ss80040305 NC_000001.8:872160:TG: NC_000001.11:896917:TG: (self)
ss255892657, ss287939384, ss294562339, ss325997504, ss550899148, ss550903136, ss552739023, ss1584129761 NC_000001.9:822160:TG: NC_000001.11:896917:TG: (self)
5984, 778, 120264, 1554, 24474, 778, 156, ss498763860, ss663209354, ss666080088, ss1367645468, ss1573868295, ss1700143187, ss1700153739, ss1793709389, ss2030297756, ss2321506829, ss2624264890, ss2750645575, ss2986150524, ss3644051501, ss3726716689, ss3783302473, ss3788980136, ss3793852696, ss3825981596, ss3836378521, ss5142055167 NC_000001.10:832297:TG: NC_000001.11:896917:TG: (self)
77834, 8788, 25657, 53570, 6133971479, ss3063573539, ss3064386050, ss3066412844, ss3646581343, ss3685992932, ss3798744173, ss3841782535, ss3943630787, ss4436447235 NC_000001.11:896917:TG: NC_000001.11:896917:TG: (self)
ss41278923, ss95218905, ss103475671, ss229263669 NT_004350.19:310929:TG: NC_000001.11:896917:TG: (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 rs34017275

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