Name: rs59306077
Published: September 21, 2022
License: Open Access

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 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:833759-833760 (GRCh38.p14) 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=0.14909 (4213/28258, 14KJPN) (+ 11 more)
delAT=0.20038 (3711/18520, ALFA)
delAT=0.14863 (2491/16760, 8.3KJPN)
delAT=0.2428 (1555/6404, 1000G_30x)
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

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: 20230706150541

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

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
14KJPN	JAPANESE	Study-wide	28258	AT=0.85091	delAT=0.14909
Allele Frequency Aggregator	Total	Global	18520	AT=0.79962	delAT=0.20038
Allele Frequency Aggregator	European	Sub	14152	AT=0.85112	delAT=0.14888
Allele Frequency Aggregator	African	Sub	2898	AT=0.5466	delAT=0.4534
Allele Frequency Aggregator	Latin American 2	Sub	610	AT=0.820	delAT=0.180
Allele Frequency Aggregator	Other	Sub	504	AT=0.762	delAT=0.238
Allele Frequency Aggregator	Latin American 1	Sub	146	AT=0.726	delAT=0.274
Allele Frequency Aggregator	Asian	Sub	112	AT=0.902	delAT=0.098
Allele Frequency Aggregator	South Asian	Sub	98	AT=0.91	delAT=0.09
8.3KJPN	JAPANESE	Study-wide	16760	AT=0.85137	delAT=0.14863
1000Genomes_30x	Global	Study-wide	6404	AT=0.7572	delAT=0.2428
1000Genomes_30x	African	Sub	1786	AT=0.5011	delAT=0.4989
1000Genomes_30x	Europe	Sub	1266	AT=0.8776	delAT=0.1224
1000Genomes_30x	South Asian	Sub	1202	AT=0.8245	delAT=0.1755
1000Genomes_30x	East Asian	Sub	1170	AT=0.8923	delAT=0.1077
1000Genomes_30x	American	Sub	980	AT=0.824	delAT=0.176
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

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.p14 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

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

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.p14 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

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#.

39 SubSNP, 14 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	GNOMAD	ss2750638531	Nov 08, 2017 (151)
20	SWEGEN	ss2986149012	Nov 08, 2017 (151)
21	MCHAISSO	ss3063573495	Nov 08, 2017 (151)
22	EVA_DECODE	ss3685992101	Jul 12, 2019 (153)
23	ACPOP	ss3726716359	Jul 12, 2019 (153)
24	KHV_HUMAN_GENOMES	ss3798743574	Jul 12, 2019 (153)
25	EVA	ss3825981456	Apr 25, 2020 (154)
26	EVA	ss3836378408	Apr 25, 2020 (154)
27	EVA	ss3841782409	Apr 25, 2020 (154)
28	KOGIC	ss3943629545	Apr 25, 2020 (154)
29	TOPMED	ss4436432699	Apr 25, 2021 (155)
30	TOMMO_GENOMICS	ss5142051989	Apr 25, 2021 (155)
31	1000G_HIGH_COVERAGE	ss5240863281	Oct 12, 2022 (156)
32	HUGCELL_USP	ss5442112220	Oct 12, 2022 (156)
33	1000G_HIGH_COVERAGE	ss5512487935	Oct 12, 2022 (156)
34	SANFORD_IMAGENETICS	ss5624749189	Oct 12, 2022 (156)
35	TOMMO_GENOMICS	ss5666191260	Oct 12, 2022 (156)
36	YY_MCH	ss5800243713	Oct 12, 2022 (156)
37	EVA	ss5831418289	Oct 12, 2022 (156)
38	EVA	ss5906704664	Oct 12, 2022 (156)
39	EVA	ss5936582588	Oct 12, 2022 (156)
40	1000Genomes	NC_000001.10 - 769139	Oct 11, 2018 (152)
41	1000Genomes_30x	NC_000001.11 - 833759	Oct 12, 2022 (156)
42	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 769139	Oct 11, 2018 (152)
43	The Danish reference pan genome	NC_000001.10 - 769139	Apr 25, 2020 (154)
44	gnomAD - Genomes	NC_000001.11 - 833759	Apr 25, 2021 (155)
45	Genome of the Netherlands Release 5	NC_000001.10 - 769139	Apr 25, 2020 (154)
46	Korean Genome Project	NC_000001.11 - 833759	Apr 25, 2020 (154)
47	Northern Sweden	NC_000001.10 - 769139	Jul 12, 2019 (153)
48	8.3KJPN	NC_000001.10 - 769139	Apr 25, 2021 (155)
49	14KJPN	NC_000001.11 - 833759	Oct 12, 2022 (156)
50	TopMed	NC_000001.11 - 833759	Apr 25, 2021 (155)
51	UK 10K study - Twins	NC_000001.10 - 769139	Oct 11, 2018 (152)
52	A Vietnamese Genetic Variation Database	NC_000001.10 - 769139	Jul 12, 2019 (153)
53	ALFA	NC_000001.11 - 833759	Apr 25, 2021 (155)

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, ss2750638531, ss2986149012, ss3726716359, ss3825981456, ss3836378408, ss5142051989, ss5624749189, ss5831418289, ss5936582588	NC_000001.10:769138:AT:	NC_000001.11:833758:AT:	(self)
13870, 64822, 7546, 28364, 39034, 4251781762, ss3063573495, ss3685992101, ss3798743574, ss3841782409, ss3943629545, ss4436432699, ss5240863281, ss5442112220, ss5512487935, ss5666191260, ss5800243713, ss5906704664	NC_000001.11:833758:AT:	NC_000001.11:833758:AT:	(self)

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

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs59306077