Name: rs201479702
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.

rs201479702

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:167670523-167670526 (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: dupG
Variation Type: Indel Insertion and Deletion
Frequency: dupG=0.013998 (3705/264690, TOPMED)
dupG=0.013352 (1872/140208, GnomAD)
dupG=0.05705 (1612/28258, 14KJPN) (+ 10 more)
dupG=0.01604 (297/18520, ALFA)
dupG=0.05829 (977/16760, 8.3KJPN)
dupG=0.0304 (195/6404, 1000G_30x)
dupG=0.0176 (79/4480, Estonian)
dupG=0.0179 (69/3854, ALSPAC)
dupG=0.0143 (53/3708, TWINSUK)
dupG=0.0262 (48/1832, Korea1K)
dupG=0.015 (15/998, GoNL)
dupG=0.012 (7/600, NorthernSweden)
dupG=0.019 (4/214, Vietnamese)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC02538 : Non Coding Transcript 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18520	GGGG=0.98396	GGGGG=0.01604	0.968251	0.000324	0.031425	0
European	Sub	14152	GGGG=0.98184	GGGGG=0.01816	0.964104	0.000424	0.035472	0
African	Sub	2898	GGGG=0.9931	GGGGG=0.0069	0.986197	0.0	0.013803	0
African Others	Sub	114	GGGG=1.000	GGGGG=0.000	1.0	0.0	0.0	N/A
African American	Sub	2784	GGGG=0.9928	GGGGG=0.0072	0.985632	0.0	0.014368	0
Asian	Sub	112	GGGG=0.991	GGGGG=0.009	0.982143	0.0	0.017857	0
East Asian	Sub	86	GGGG=0.99	GGGGG=0.01	0.976744	0.0	0.023256	0
Other Asian	Sub	26	GGGG=1.00	GGGGG=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	146	GGGG=0.993	GGGGG=0.007	0.986301	0.0	0.013699	0
Latin American 2	Sub	610	GGGG=0.992	GGGGG=0.008	0.983607	0.0	0.016393	0
South Asian	Sub	98	GGGG=0.92	GGGGG=0.08	0.836735	0.0	0.163265	0
Other	Sub	504	GGGG=0.990	GGGGG=0.010	0.980159	0.0	0.019841	0

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	- No frequency provided	dupG=0.013998
gnomAD - Genomes	Global	Study-wide	140208	- No frequency provided	dupG=0.013352
gnomAD - Genomes	European	Sub	75916	- No frequency provided	dupG=0.01508
gnomAD - Genomes	African	Sub	42030	- No frequency provided	dupG=0.00680
gnomAD - Genomes	American	Sub	13654	- No frequency provided	dupG=0.01531
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	- No frequency provided	dupG=0.0337
gnomAD - Genomes	East Asian	Sub	3134	- No frequency provided	dupG=0.0262
gnomAD - Genomes	Other	Sub	2152	- No frequency provided	dupG=0.0177
14KJPN	JAPANESE	Study-wide	28258	- No frequency provided	dupG=0.05705
Allele Frequency Aggregator	Total	Global	18520	(G)₄=0.98396	dupG=0.01604
Allele Frequency Aggregator	European	Sub	14152	(G)₄=0.98184	dupG=0.01816
Allele Frequency Aggregator	African	Sub	2898	(G)₄=0.9931	dupG=0.0069
Allele Frequency Aggregator	Latin American 2	Sub	610	(G)₄=0.992	dupG=0.008
Allele Frequency Aggregator	Other	Sub	504	(G)₄=0.990	dupG=0.010
Allele Frequency Aggregator	Latin American 1	Sub	146	(G)₄=0.993	dupG=0.007
Allele Frequency Aggregator	Asian	Sub	112	(G)₄=0.991	dupG=0.009
Allele Frequency Aggregator	South Asian	Sub	98	(G)₄=0.92	dupG=0.08
8.3KJPN	JAPANESE	Study-wide	16760	- No frequency provided	dupG=0.05829
1000Genomes_30x	Global	Study-wide	6404	- No frequency provided	dupG=0.0304
1000Genomes_30x	African	Sub	1786	- No frequency provided	dupG=0.0050
1000Genomes_30x	Europe	Sub	1266	- No frequency provided	dupG=0.0190
1000Genomes_30x	South Asian	Sub	1202	- No frequency provided	dupG=0.1007
1000Genomes_30x	East Asian	Sub	1170	- No frequency provided	dupG=0.0188
1000Genomes_30x	American	Sub	980	- No frequency provided	dupG=0.019
Genetic variation in the Estonian population	Estonian	Study-wide	4480	- No frequency provided	dupG=0.0176
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	- No frequency provided	dupG=0.0179
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	- No frequency provided	dupG=0.0143
Korean Genome Project	KOREAN	Study-wide	1832	- No frequency provided	dupG=0.0262
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	- No frequency provided	dupG=0.015
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	dupG=0.012
A Vietnamese Genetic Variation Database	Global	Study-wide	214	- No frequency provided	dupG=0.019

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 6	NC_000006.12:g.167670526dup
GRCh37.p13 chr 6	NC_000006.11:g.168071206dup

Gene: LINC02538, long intergenic non-protein coding RNA 2538 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC02538 transcript	NR_117091.1:n.839dup	N/A	Non Coding Transcript 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	(G)₄=	dupG
GRCh38.p14 chr 6	NC_000006.12:g.167670523_167670526=	NC_000006.12:g.167670526dup
GRCh37.p13 chr 6	NC_000006.11:g.168071203_168071206=	NC_000006.11:g.168071206dup
LINC02538 transcript	NR_117091.1:n.836_839=	NR_117091.1:n.839dup
LOC401286 transcript	NM_001023565.1:c.-886_-883=	NM_001023565.1:c.-883dup

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#.

28 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss499737967	May 04, 2012 (137)
2	SSMP	ss663675317	Apr 01, 2015 (144)
3	EVA-GONL	ss983792610	Aug 21, 2014 (142)
4	EVA_DECODE	ss1593366553	Apr 01, 2015 (144)
5	EVA_UK10K_ALSPAC	ss1705473303	Apr 01, 2015 (144)
6	EVA_UK10K_TWINSUK	ss1705473326	Apr 01, 2015 (144)
7	JJLAB	ss2030813674	Sep 14, 2016 (149)
8	ILLUMINA	ss2711099552	Nov 08, 2017 (151)
9	GNOMAD	ss2848202985	Nov 08, 2017 (151)
10	SWEGEN	ss3000392756	Nov 08, 2017 (151)
11	EGCUT_WGS	ss3668332144	Jul 13, 2019 (153)
12	EVA_DECODE	ss3718821933	Jul 13, 2019 (153)
13	ACPOP	ss3734228572	Jul 13, 2019 (153)
14	KHV_HUMAN_GENOMES	ss3809178650	Jul 13, 2019 (153)
15	KOGIC	ss3960609340	Apr 26, 2020 (154)
16	TOPMED	ss4731107712	Apr 26, 2021 (155)
17	TOMMO_GENOMICS	ss5181160927	Apr 26, 2021 (155)
18	1000G_HIGH_COVERAGE	ss5271319378	Oct 13, 2022 (156)
19	HUGCELL_USP	ss5468672148	Oct 13, 2022 (156)
20	1000G_HIGH_COVERAGE	ss5558737505	Oct 13, 2022 (156)
21	SANFORD_IMAGENETICS	ss5642050230	Oct 13, 2022 (156)
22	TOMMO_GENOMICS	ss5720403384	Oct 13, 2022 (156)
23	YY_MCH	ss5808202209	Oct 13, 2022 (156)
24	EVA	ss5843371304	Oct 13, 2022 (156)
25	EVA	ss5855702228	Oct 13, 2022 (156)
26	EVA	ss5887068878	Oct 13, 2022 (156)
27	EVA	ss5971204810	Oct 13, 2022 (156)
28	EVA	ss5971204811	Oct 13, 2022 (156)
29	1000Genomes_30x	NC_000006.12 - 167670523	Oct 13, 2022 (156)
30	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 168071203	Oct 12, 2018 (152)
31	Genetic variation in the Estonian population	NC_000006.11 - 168071203	Oct 12, 2018 (152)
32	gnomAD - Genomes	NC_000006.12 - 167670523	Apr 26, 2021 (155)
33	Genome of the Netherlands Release 5	NC_000006.11 - 168071203	Apr 26, 2020 (154)
34	Korean Genome Project	NC_000006.12 - 167670523	Apr 26, 2020 (154)
35	Northern Sweden	NC_000006.11 - 168071203	Jul 13, 2019 (153)
36	8.3KJPN	NC_000006.11 - 168071203	Apr 26, 2021 (155)
37	14KJPN	NC_000006.12 - 167670523	Oct 13, 2022 (156)
38	TopMed	NC_000006.12 - 167670523	Apr 26, 2021 (155)
39	UK 10K study - Twins	NC_000006.11 - 168071203	Oct 12, 2018 (152)
40	A Vietnamese Genetic Variation Database	NC_000006.11 - 168071203	Jul 13, 2019 (153)
41	ALFA	NC_000006.12 - 167670523	Apr 26, 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)
rs372674498	May 15, 2013 (138)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1593366553	NC_000006.10:167814051::G	NC_000006.12:167670522:GGGG:GGGGG	(self)
19680692, 14070392, 8760076, 7513437, 39130234, 19680692, 4381746, ss499737967, ss663675317, ss983792610, ss1705473303, ss1705473326, ss2030813674, ss2848202985, ss3000392756, ss3668332144, ss3734228572, ss5181160927, ss5642050230, ss5843371304, ss5971204810, ss5971204811	NC_000006.11:168071202::G	NC_000006.12:167670522:GGGG:GGGGG	(self)
ss2711099552	NC_000006.11:168071203::G	NC_000006.12:167670522:GGGG:GGGGG	(self)
46263440, 248971669, 16987341, 54240488, 568485270, ss3718821933, ss3809178650, ss3960609340, ss4731107712, ss5271319378, ss5468672148, ss5558737505, ss5720403384, ss5808202209, ss5855702228, ss5887068878	NC_000006.12:167670522::G	NC_000006.12:167670522:GGGG:GGGGG	(self)
10736746982	NC_000006.12:167670522:GGGG:GGGGG	NC_000006.12:167670522:GGGG:GGGGG	(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 rs201479702

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs201479702