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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.

rs59306077

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:833759-833760 (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
delAT
Variation Type
Deletion
Frequency
delAT=0.240610 (63687/264690, TOPMED)
delAT=0.241420 (33708/139624, GnomAD)
delAT=0.20038 (3711/18520, ALFA) (+ 9 more)
delAT=0.14863 (2491/16760, 8.3KJPN)
delAT=0.2332 (1168/5008, 1000G)
delAT=0.1230 (474/3854, ALSPAC)
delAT=0.1289 (478/3708, TWINSUK)
delAT=0.1556 (285/1832, Korea1K)
delAT=0.146 (146/998, GoNL)
delAT=0.135 (81/600, NorthernSweden)
delAT=0.084 (18/214, Vietnamese)
delAT=0.03 (1/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01128 : 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.833759_833760del
GRCh37.p13 chr 1 NC_000001.10:g.769139_769140del
Gene: LINC01128, long intergenic non-protein coding RNA 1128 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01128 transcript variant 1 NR_047519.1:n. N/A Intron Variant
LINC01128 transcript variant 3 NR_047521.1:n. N/A Intron Variant
LINC01128 transcript variant 5 NR_047523.1:n. N/A Intron Variant
LINC01128 transcript variant 7 NR_047524.1:n. N/A Intron Variant
LINC01128 transcript variant 8 NR_047525.1:n. N/A Intron Variant
LINC01128 transcript variant 9 NR_047526.1: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 18520 AT=0.79962 =0.20038
European Sub 14152 AT=0.85112 =0.14888
African Sub 2898 AT=0.5466 =0.4534
African Others Sub 114 AT=0.518 =0.482
African American Sub 2784 AT=0.5478 =0.4522
Asian Sub 112 AT=0.902 =0.098
East Asian Sub 86 AT=0.91 =0.09
Other Asian Sub 26 AT=0.88 =0.12
Latin American 1 Sub 146 AT=0.726 =0.274
Latin American 2 Sub 610 AT=0.820 =0.180
South Asian Sub 98 AT=0.91 =0.09
Other Sub 504 AT=0.762 =0.238


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 AT=0.759390 delAT=0.240610
gnomAD - Genomes Global Study-wide 139624 AT=0.758580 delAT=0.241420
gnomAD - Genomes European Sub 75800 AT=0.85100 delAT=0.14900
gnomAD - Genomes African Sub 41686 AT=0.55057 delAT=0.44943
gnomAD - Genomes American Sub 13550 AT=0.81845 delAT=0.18155
gnomAD - Genomes Ashkenazi Jewish Sub 3322 AT=0.8534 delAT=0.1466
gnomAD - Genomes East Asian Sub 3122 AT=0.9058 delAT=0.0942
gnomAD - Genomes Other Sub 2144 AT=0.7957 delAT=0.2043
8.3KJPN JAPANESE Study-wide 16760 AT=0.85137 delAT=0.14863
1000Genomes Global Study-wide 5008 AT=0.7668 delAT=0.2332
1000Genomes African Sub 1322 AT=0.5068 delAT=0.4932
1000Genomes East Asian Sub 1008 AT=0.8958 delAT=0.1042
1000Genomes Europe Sub 1006 AT=0.8757 delAT=0.1243
1000Genomes South Asian Sub 978 AT=0.827 delAT=0.173
1000Genomes American Sub 694 AT=0.831 delAT=0.169
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 AT=0.8770 delAT=0.1230
UK 10K study - Twins TWIN COHORT Study-wide 3708 AT=0.8711 delAT=0.1289
Korean Genome Project KOREAN Study-wide 1832 AT=0.8444 delAT=0.1556
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 AT=0.854 delAT=0.146
Northern Sweden ACPOP Study-wide 600 AT=0.865 delAT=0.135
A Vietnamese Genetic Variation Database Global Study-wide 214 AT=0.916 delAT=0.084
The Danish reference pan genome Danish Study-wide 40 AT=0.97 delAT=0.03
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 AT= delAT
GRCh38.p13 chr 1 NC_000001.11:g.833759_833760= NC_000001.11:g.833759_833760del
GRCh37.p13 chr 1 NC_000001.10:g.769139_769140= NC_000001.10:g.769139_769140del
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#.

32 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 HGSV ss83547739 Dec 15, 2007 (129)
2 GMI ss287939301 May 04, 2012 (137)
3 1000GENOMES ss325997444 May 09, 2011 (135)
4 1000GENOMES ss498763828 May 04, 2012 (137)
5 LUNTER ss550899127 Apr 25, 2013 (138)
6 LUNTER ss550903122 Apr 25, 2013 (138)
7 LUNTER ss552738987 Apr 25, 2013 (138)
8 TISHKOFF ss553708523 Apr 25, 2013 (138)
9 SSMP ss663205229 Apr 01, 2015 (144)
10 BILGI_BIOE ss666079984 Apr 25, 2013 (138)
11 EVA-GONL ss974769350 Aug 21, 2014 (142)
12 1000GENOMES ss1367645377 Aug 21, 2014 (142)
13 EVA_GENOME_DK ss1573867864 Apr 01, 2015 (144)
14 EVA_DECODE ss1584129484 Apr 01, 2015 (144)
15 EVA_UK10K_ALSPAC ss1700142320 Apr 01, 2015 (144)
16 EVA_UK10K_TWINSUK ss1700153430 Apr 01, 2015 (144)
17 HAMMER_LAB ss1793705773 Sep 08, 2015 (146)
18 JJLAB ss2030297730 Sep 14, 2016 (149)
19 TOPMED ss2321503418 Dec 20, 2016 (150)
20 GNOMAD ss2750638531 Nov 08, 2017 (151)
21 SWEGEN ss2986149012 Nov 08, 2017 (151)
22 MCHAISSO ss3063573495 Nov 08, 2017 (151)
23 TOPMED ss3066399528 Nov 08, 2017 (151)
24 EVA_DECODE ss3685992101 Jul 12, 2019 (153)
25 ACPOP ss3726716359 Jul 12, 2019 (153)
26 KHV_HUMAN_GENOMES ss3798743574 Jul 12, 2019 (153)
27 EVA ss3825981456 Apr 25, 2020 (154)
28 EVA ss3836378408 Apr 25, 2020 (154)
29 EVA ss3841782409 Apr 25, 2020 (154)
30 KOGIC ss3943629545 Apr 25, 2020 (154)
31 TOPMED ss4436432699 Apr 25, 2021 (155)
32 TOMMO_GENOMICS ss5142051989 Apr 25, 2021 (155)
33 1000Genomes NC_000001.10 - 769139 Oct 11, 2018 (152)
34 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 769139 Oct 11, 2018 (152)
35 The Danish reference pan genome NC_000001.10 - 769139 Apr 25, 2020 (154)
36 gnomAD - Genomes NC_000001.11 - 833759 Apr 25, 2021 (155)
37 Genome of the Netherlands Release 5 NC_000001.10 - 769139 Apr 25, 2020 (154)
38 Korean Genome Project NC_000001.11 - 833759 Apr 25, 2020 (154)
39 Northern Sweden NC_000001.10 - 769139 Jul 12, 2019 (153)
40 8.3KJPN NC_000001.10 - 769139 Apr 25, 2021 (155)
41 TopMed NC_000001.11 - 833759 Apr 25, 2021 (155)
42 UK 10K study - Twins NC_000001.10 - 769139 Oct 11, 2018 (152)
43 A Vietnamese Genetic Variation Database NC_000001.10 - 769139 Jul 12, 2019 (153)
44 ALFA NC_000001.11 - 833759 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)
rs150438435 Sep 17, 2011 (135)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83547739 NC_000001.8:809001:AT: NC_000001.11:833758:AT: (self)
ss287939301, ss325997444, ss550899127, ss550903122, ss552738987, ss1584129484 NC_000001.9:759001:AT: NC_000001.11:833758:AT: (self)
3994, 283, 120244, 399, 1224, 21296, 283, 57, ss498763828, ss553708523, ss663205229, ss666079984, ss974769350, ss1367645377, ss1573867864, ss1700142320, ss1700153430, ss1793705773, ss2030297730, ss2321503418, ss2750638531, ss2986149012, ss3726716359, ss3825981456, ss3836378408, ss5142051989 NC_000001.10:769138:AT: NC_000001.11:833758:AT: (self)
64822, 7546, 16764, 39034, 4251781762, ss3063573495, ss3066399528, ss3685992101, ss3798743574, ss3841782409, ss3943629545, ss4436432699 NC_000001.11:833758:AT: NC_000001.11:833758:AT: (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 rs59306077

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