Name: rs72215351
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.

rs72215351

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:8411248-8411250 (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: delTA / dupTA
Variation Type: Indel Insertion and Deletion
Frequency: delTA=0.092266 (24422/264690, TOPMED)
delTA=0.094006 (13061/138938, GnomAD)
delTA=0.00336 (95/28258, 14KJPN) (+ 10 more)
delTA=0.00310 (52/16760, 8.3KJPN)
delTA=0.09717 (1587/16332, ALFA)
delTA=0.0835 (418/5008, 1000G)
delTA=0.0864 (387/4480, Estonian)
delTA=0.1380 (532/3854, ALSPAC)
delTA=0.1486 (551/3708, TWINSUK)
delTA=0.0093 (17/1832, Korea1K)
delTA=0.148 (148/998, GoNL)
delTA=0.115 (69/598, NorthernSweden)
delTA=0.12 (5/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC02226 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	16332	ATA=0.90283	A=0.09717	0.817904	0.012246	0.169851	5
European	Sub	12080	ATA=0.88510	A=0.11490	0.78543	0.015232	0.199338	2
African	Sub	2816	ATA=0.9748	A=0.0252	0.949574	0.0	0.050426	1
African Others	Sub	108	ATA=1.000	A=0.000	1.0	0.0	0.0	N/A
African American	Sub	2708	ATA=0.9738	A=0.0262	0.947563	0.0	0.052437	1
Asian	Sub	108	ATA=1.000	A=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	84	ATA=1.00	A=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	24	ATA=1.00	A=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	146	ATA=0.897	A=0.103	0.808219	0.013699	0.178082	0
Latin American 2	Sub	610	ATA=0.915	A=0.085	0.836066	0.006557	0.157377	0
South Asian	Sub	94	ATA=0.84	A=0.16	0.702128	0.021277	0.276596	0
Other	Sub	478	ATA=0.904	A=0.096	0.824268	0.016736	0.158996	1

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	ATA=0.907734	delTA=0.092266
gnomAD - Genomes	Global	Study-wide	138938	ATA=0.905994	delTA=0.094006
gnomAD - Genomes	European	Sub	75104	ATA=0.87214	delTA=0.12786
gnomAD - Genomes	African	Sub	41710	ATA=0.97262	delTA=0.02738
gnomAD - Genomes	American	Sub	13566	ATA=0.88383	delTA=0.11617
gnomAD - Genomes	Ashkenazi Jewish	Sub	3308	ATA=0.8567	delTA=0.1433
gnomAD - Genomes	East Asian	Sub	3122	ATA=0.9859	delTA=0.0141
gnomAD - Genomes	Other	Sub	2128	ATA=0.8957	delTA=0.1043
14KJPN	JAPANESE	Study-wide	28258	ATA=0.99664	delTA=0.00336
8.3KJPN	JAPANESE	Study-wide	16760	ATA=0.99690	delTA=0.00310
Allele Frequency Aggregator	Total	Global	16332	ATA=0.90283	delTA=0.09717
Allele Frequency Aggregator	European	Sub	12080	ATA=0.88510	delTA=0.11490
Allele Frequency Aggregator	African	Sub	2816	ATA=0.9748	delTA=0.0252
Allele Frequency Aggregator	Latin American 2	Sub	610	ATA=0.915	delTA=0.085
Allele Frequency Aggregator	Other	Sub	478	ATA=0.904	delTA=0.096
Allele Frequency Aggregator	Latin American 1	Sub	146	ATA=0.897	delTA=0.103
Allele Frequency Aggregator	Asian	Sub	108	ATA=1.000	delTA=0.000
Allele Frequency Aggregator	South Asian	Sub	94	ATA=0.84	delTA=0.16
1000Genomes	Global	Study-wide	5008	ATA=0.9165	delTA=0.0835
1000Genomes	African	Sub	1322	ATA=0.9924	delTA=0.0076
1000Genomes	East Asian	Sub	1008	ATA=0.9871	delTA=0.0129
1000Genomes	Europe	Sub	1006	ATA=0.8658	delTA=0.1342
1000Genomes	South Asian	Sub	978	ATA=0.798	delTA=0.202
1000Genomes	American	Sub	694	ATA=0.911	delTA=0.089
Genetic variation in the Estonian population	Estonian	Study-wide	4480	ATA=0.9136	delTA=0.0864
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	ATA=0.8620	delTA=0.1380
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	ATA=0.8514	delTA=0.1486
Korean Genome Project	KOREAN	Study-wide	1832	ATA=0.9907	delTA=0.0093
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	ATA=0.852	delTA=0.148
Northern Sweden	ACPOP	Study-wide	598	ATA=0.885	delTA=0.115
The Danish reference pan genome	Danish	Study-wide	40	ATA=0.88	delTA=0.12

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 5	NC_000005.10:g.8411249_8411250del
GRCh38.p14 chr 5	NC_000005.10:g.8411249_8411250dup
GRCh37.p13 chr 5	NC_000005.9:g.8411362_8411363del
GRCh37.p13 chr 5	NC_000005.9:g.8411362_8411363dup

Gene: LINC02226, long intergenic non-protein coding RNA 2226 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC02226 transcript	NR_039984.1: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	ATA=	delTA	dupTA
GRCh38.p14 chr 5	NC_000005.10:g.8411248_8411250=	NC_000005.10:g.8411249_8411250del	NC_000005.10:g.8411249_8411250dup
GRCh37.p13 chr 5	NC_000005.9:g.8411361_8411363=	NC_000005.9:g.8411362_8411363del	NC_000005.9:g.8411362_8411363dup

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#.

40 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ABI	ss42583474	Oct 12, 2018 (152)
2	1000GENOMES	ss326672794	May 09, 2011 (135)
3	LUNTER	ss551469622	Apr 25, 2013 (138)
4	TISHKOFF	ss554162966	Jan 10, 2018 (151)
5	SSMP	ss663626101	Apr 01, 2015 (144)
6	BILGI_BIOE	ss666298684	Apr 25, 2013 (138)
7	EVA-GONL	ss981229198	Aug 21, 2014 (142)
8	1000GENOMES	ss1373407438	Aug 21, 2014 (142)
9	DDI	ss1536450965	Apr 01, 2015 (144)
10	EVA_GENOME_DK	ss1576455301	Apr 01, 2015 (144)
11	EVA_DECODE	ss1590744824	Apr 01, 2015 (144)
12	EVA_UK10K_ALSPAC	ss1704554240	Apr 01, 2015 (144)
13	EVA_UK10K_TWINSUK	ss1704554274	Apr 01, 2015 (144)
14	JJLAB	ss2030664173	Sep 14, 2016 (149)
15	GNOMAD	ss2820952439	Nov 08, 2017 (151)
16	SWEGEN	ss2996410044	Nov 08, 2017 (151)
17	BEROUKHIMLAB	ss3644178161	Oct 12, 2018 (152)
18	BIOINF_KMB_FNS_UNIBA	ss3645859124	Oct 12, 2018 (152)
19	EGCUT_WGS	ss3664299781	Jul 13, 2019 (153)
20	EVA_DECODE	ss3714069896	Jul 13, 2019 (153)
21	ACPOP	ss3732073103	Jul 13, 2019 (153)
22	PACBIO	ss3785018702	Jul 13, 2019 (153)
23	PACBIO	ss3790437456	Jul 13, 2019 (153)
24	PACBIO	ss3795313993	Jul 13, 2019 (153)
25	KHV_HUMAN_GENOMES	ss3806211293	Jul 13, 2019 (153)
26	EVA	ss3829085260	Apr 26, 2020 (154)
27	EVA	ss3838004932	Apr 26, 2020 (154)
28	EVA	ss3843444596	Apr 26, 2020 (154)
29	KOGIC	ss3956063360	Apr 26, 2020 (154)
30	TOPMED	ss4649000913	Apr 26, 2021 (155)
31	TOMMO_GENOMICS	ss5170302422	Apr 26, 2021 (155)
32	1000G_HIGH_COVERAGE	ss5262815212	Oct 13, 2022 (156)
33	HUGCELL_USP	ss5461166789	Oct 13, 2022 (156)
34	SANFORD_IMAGENETICS	ss5637148537	Oct 13, 2022 (156)
35	TOMMO_GENOMICS	ss5705953920	Oct 13, 2022 (156)
36	YY_MCH	ss5806005672	Oct 13, 2022 (156)
37	EVA	ss5834494733	Oct 13, 2022 (156)
38	EVA	ss5892919663	Oct 13, 2022 (156)
39	EVA	ss5965558355	Oct 13, 2022 (156)
40	EVA	ss5980278635	Oct 13, 2022 (156)
41	1000Genomes	NC_000005.9 - 8411361	Oct 12, 2018 (152)
42	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 8411361	Oct 12, 2018 (152)
43	Genetic variation in the Estonian population	NC_000005.9 - 8411361	Oct 12, 2018 (152)
44	The Danish reference pan genome	NC_000005.9 - 8411361	Apr 26, 2020 (154)
45	gnomAD - Genomes	NC_000005.10 - 8411248	Apr 26, 2021 (155)
46	Genome of the Netherlands Release 5	NC_000005.9 - 8411361	Apr 26, 2020 (154)
47	Korean Genome Project	NC_000005.10 - 8411248	Apr 26, 2020 (154)
48	Northern Sweden	NC_000005.9 - 8411361	Jul 13, 2019 (153)
49	8.3KJPN	NC_000005.9 - 8411361	Apr 26, 2021 (155)
50	14KJPN	NC_000005.10 - 8411248	Oct 13, 2022 (156)
51	TopMed	NC_000005.10 - 8411248	Apr 26, 2021 (155)
52	UK 10K study - Twins	NC_000005.9 - 8411361	Oct 12, 2018 (152)
53	ALFA	NC_000005.10 - 8411248	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)
rs150275725	Sep 17, 2011 (135)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss326672794, ss551469622, ss1590744824	NC_000005.8:8464360:AT:	NC_000005.10:8411247:ATA:A	(self)
25385863, 14123863, 10038029, 976276, 6270843, 5357968, 28271729, 14123863, ss663626101, ss666298684, ss981229198, ss1373407438, ss1576455301, ss1704554240, ss1704554274, ss2030664173, ss2820952439, ss2996410044, ss3644178161, ss3664299781, ss3732073103, ss3785018702, ss3790437456, ss3795313993, ss3829085260, ss3838004932, ss5170302422, ss5637148537, ss5834494733, ss5965558355, ss5980278635	NC_000005.9:8411360:AT:	NC_000005.10:8411247:ATA:A	(self)
ss554162966	NC_000005.9:8411361:TA:	NC_000005.10:8411247:ATA:A	(self)
179416145, 12441361, 39791024, 486378470, ss3645859124, ss3714069896, ss3806211293, ss3843444596, ss3956063360, ss4649000913, ss5262815212, ss5461166789, ss5705953920, ss5806005672, ss5892919663	NC_000005.10:8411247:AT:	NC_000005.10:8411247:ATA:A	(self)
9248671480	NC_000005.10:8411247:ATA:A	NC_000005.10:8411247:ATA:A	(self)
ss42583474	NT_006576.16:8401361:TA:	NC_000005.10:8411247:ATA:A	(self)
ss1536450965	NC_000005.9:8411360::AT	NC_000005.10:8411247:ATA:ATATA	(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 rs72215351

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

rs72215351