Name: rs250
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.

rs250

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr8:19953513-19953518 (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: dupTG
Variation Type: Indel Insertion and Deletion
Frequency: dupTG=0.221508 (58631/264690, TOPMED)
dupTG=0.211823 (29659/140018, GnomAD)
dupTG=0.15606 (4410/28258, 14KJPN) (+ 12 more)
dupTG=0.16226 (3017/18594, ALFA)
dupTG=0.15895 (2664/16760, 8.3KJPN)
dupTG=0.2413 (1545/6404, 1000G_30x)
dupTG=0.2338 (1171/5008, 1000G)
dupTG=0.0891 (399/4480, Estonian)
dupTG=0.1238 (477/3854, ALSPAC)
dupTG=0.1273 (472/3708, TWINSUK)
dupTG=0.1310 (240/1832, Korea1K)
dupTG=0.103 (103/998, GoNL)
dupTG=0.083 (50/600, NorthernSweden)
dupTG=0.159 (34/214, Vietnamese)
dupTG=0.12 (5/40, GENOME_DK)

Clinical Significance: Reported in ClinVar
Gene : Consequence: LPL : 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	18594	TGTGTG=0.83774	TGTGTGTG=0.16226	0.709906	0.03442	0.255674	18
European	Sub	14202	TGTGTG=0.88593	TGTGTGTG=0.11407	0.785664	0.013801	0.200535	0
African	Sub	2912	TGTGTG=0.6216	TGTGTGTG=0.3784	0.377747	0.134615	0.487637	1
African Others	Sub	114	TGTGTG=0.623	TGTGTGTG=0.377	0.473684	0.22807	0.298246	5
African American	Sub	2798	TGTGTG=0.6215	TGTGTGTG=0.3785	0.373838	0.130808	0.495354	3
Asian	Sub	112	TGTGTG=0.786	TGTGTGTG=0.214	0.589286	0.017857	0.392857	1
East Asian	Sub	86	TGTGTG=0.79	TGTGTGTG=0.21	0.604651	0.023256	0.372093	0
Other Asian	Sub	26	TGTGTG=0.77	TGTGTGTG=0.23	0.538462	0.0	0.461538	1
Latin American 1	Sub	146	TGTGTG=0.801	TGTGTGTG=0.199	0.643836	0.041096	0.315068	0
Latin American 2	Sub	610	TGTGTG=0.838	TGTGTGTG=0.162	0.698361	0.022951	0.278689	0
South Asian	Sub	98	TGTGTG=0.80	TGTGTGTG=0.20	0.653061	0.061224	0.285714	0
Other	Sub	514	TGTGTG=0.761	TGTGTGTG=0.239	0.568093	0.046693	0.385214	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	- No frequency provided	dupTG=0.221508
gnomAD - Genomes	Global	Study-wide	140018	- No frequency provided	dupTG=0.211823
gnomAD - Genomes	European	Sub	75904	- No frequency provided	dupTG=0.12272
gnomAD - Genomes	African	Sub	41884	- No frequency provided	dupTG=0.38096
gnomAD - Genomes	American	Sub	13640	- No frequency provided	dupTG=0.19993
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	- No frequency provided	dupTG=0.2274
gnomAD - Genomes	East Asian	Sub	3118	- No frequency provided	dupTG=0.1559
gnomAD - Genomes	Other	Sub	2152	- No frequency provided	dupTG=0.1952
14KJPN	JAPANESE	Study-wide	28258	- No frequency provided	dupTG=0.15606
Allele Frequency Aggregator	Total	Global	18594	(TG)₃=0.83774	dupTG=0.16226
Allele Frequency Aggregator	European	Sub	14202	(TG)₃=0.88593	dupTG=0.11407
Allele Frequency Aggregator	African	Sub	2912	(TG)₃=0.6216	dupTG=0.3784
Allele Frequency Aggregator	Latin American 2	Sub	610	(TG)₃=0.838	dupTG=0.162
Allele Frequency Aggregator	Other	Sub	514	(TG)₃=0.761	dupTG=0.239
Allele Frequency Aggregator	Latin American 1	Sub	146	(TG)₃=0.801	dupTG=0.199
Allele Frequency Aggregator	Asian	Sub	112	(TG)₃=0.786	dupTG=0.214
Allele Frequency Aggregator	South Asian	Sub	98	(TG)₃=0.80	dupTG=0.20
8.3KJPN	JAPANESE	Study-wide	16760	- No frequency provided	dupTG=0.15895
1000Genomes_30x	Global	Study-wide	6404	- No frequency provided	dupTG=0.2413
1000Genomes_30x	African	Sub	1786	- No frequency provided	dupTG=0.4227
1000Genomes_30x	Europe	Sub	1266	- No frequency provided	dupTG=0.1501
1000Genomes_30x	South Asian	Sub	1202	- No frequency provided	dupTG=0.1905
1000Genomes_30x	East Asian	Sub	1170	- No frequency provided	dupTG=0.1744
1000Genomes_30x	American	Sub	980	- No frequency provided	dupTG=0.170
1000Genomes	Global	Study-wide	5008	- No frequency provided	dupTG=0.2338
1000Genomes	African	Sub	1322	- No frequency provided	dupTG=0.4115
1000Genomes	East Asian	Sub	1008	- No frequency provided	dupTG=0.1726
1000Genomes	Europe	Sub	1006	- No frequency provided	dupTG=0.1431
1000Genomes	South Asian	Sub	978	- No frequency provided	dupTG=0.194
1000Genomes	American	Sub	694	- No frequency provided	dupTG=0.171
Genetic variation in the Estonian population	Estonian	Study-wide	4480	- No frequency provided	dupTG=0.0891
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	- No frequency provided	dupTG=0.1238
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	- No frequency provided	dupTG=0.1273
Korean Genome Project	KOREAN	Study-wide	1832	- No frequency provided	dupTG=0.1310
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	- No frequency provided	dupTG=0.103
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	dupTG=0.083
A Vietnamese Genetic Variation Database	Global	Study-wide	214	- No frequency provided	dupTG=0.159
The Danish reference pan genome	Danish	Study-wide	40	- No frequency provided	dupTG=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 8	NC_000008.11:g.19953513TG[4]
GRCh37.p13 chr 8	NC_000008.10:g.19811024TG[4]
LPL RefSeqGene (LRG_1298)	NG_008855.2:g.56797TG[4]

Gene: LPL, lipoprotein lipase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LPL transcript	NM_000237.3:c.541+92TG[4]	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.

Allele: dupTG (allele ID: 1167436 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001533982.2	not provided	Benign

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)₃=	dupTG
GRCh38.p14 chr 8	NC_000008.11:g.19953513_19953518=	NC_000008.11:g.19953513TG[4]
GRCh37.p13 chr 8	NC_000008.10:g.19811024_19811029=	NC_000008.10:g.19811024TG[4]
LPL RefSeqGene (LRG_1298)	NG_008855.2:g.56797_56802=	NG_008855.2:g.56797TG[4]
LPL transcript	NM_000237.2:c.541+92=	NM_000237.2:c.541+92TG[4]
LPL transcript	NM_000237.3:c.541+92=	NM_000237.3:c.541+92TG[4]

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#.

53 SubSNP, 15 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	HGBASE	ss2419753	Dec 03, 2013 (138)
2	HGSV	ss82113717	Dec 04, 2013 (138)
3	BUSHMAN	ss193965719	Jul 04, 2010 (138)
4	GMI	ss288895653	May 04, 2012 (138)
5	GMI	ss288895654	May 04, 2012 (138)
6	1000GENOMES	ss327029962	May 09, 2011 (138)
7	1000GENOMES	ss327090017	May 09, 2011 (138)
8	1000GENOMES	ss327406283	May 09, 2011 (138)
9	1000GENOMES	ss500127589	May 04, 2012 (138)
10	LUNTER	ss551825305	Apr 25, 2013 (138)
11	LUNTER	ss552041870	Apr 25, 2013 (138)
12	LUNTER	ss553332751	Apr 25, 2013 (138)
13	TISHKOFF	ss559644561	Apr 25, 2013 (138)
14	SSMP	ss663841921	Apr 01, 2015 (144)
15	BILGI_BIOE	ss666430660	Apr 25, 2013 (138)
16	EVA-GONL	ss985272595	Aug 21, 2014 (142)
17	1000GENOMES	ss1367861529	Aug 21, 2014 (142)
18	EVA_GENOME_DK	ss1577168414	Apr 01, 2015 (144)
19	EVA_DECODE	ss1594862256	Apr 01, 2015 (144)
20	EVA_UK10K_ALSPAC	ss1705971022	Apr 01, 2015 (144)
21	EVA_UK10K_TWINSUK	ss1705971094	Apr 01, 2015 (144)
22	HAMMER_LAB	ss1805432767	Sep 08, 2015 (146)
23	JJLAB	ss2030895904	Sep 14, 2016 (149)
24	SYSTEMSBIOZJU	ss2626975135	Nov 08, 2017 (151)
25	AFFY	ss2986076160	Nov 08, 2017 (151)
26	SWEGEN	ss3002804408	Nov 08, 2017 (151)
27	MCHAISSO	ss3066191573	Nov 08, 2017 (151)
28	BIOINF_KMB_FNS_UNIBA	ss3646082947	Oct 12, 2018 (152)
29	EGCUT_WGS	ss3670484437	Jul 13, 2019 (153)
30	EVA_DECODE	ss3721555412	Jul 13, 2019 (153)
31	ACPOP	ss3735467019	Jul 13, 2019 (153)
32	KHV_HUMAN_GENOMES	ss3810881192	Jul 13, 2019 (153)
33	EVA	ss3831054889	Apr 26, 2020 (154)
34	KOGIC	ss3963402129	Apr 26, 2020 (154)
35	FSA-LAB	ss3984393685	Apr 27, 2021 (155)
36	FSA-LAB	ss3984393686	Apr 27, 2021 (155)
37	FSA-LAB	ss3984393687	Apr 27, 2021 (155)
38	EVA	ss3986415463	Apr 27, 2021 (155)
39	GNOMAD	ss4180332412	Apr 27, 2021 (155)
40	TOPMED	ss4778092345	Apr 27, 2021 (155)
41	TOMMO_GENOMICS	ss5187654352	Apr 27, 2021 (155)
42	1000G_HIGH_COVERAGE	ss5276330108	Oct 14, 2022 (156)
43	HUGCELL_USP	ss5472980734	Oct 14, 2022 (156)
44	1000G_HIGH_COVERAGE	ss5566253928	Oct 14, 2022 (156)
45	EVA	ss5624176077	Oct 14, 2022 (156)
46	SANFORD_IMAGENETICS	ss5644923806	Oct 14, 2022 (156)
47	TOMMO_GENOMICS	ss5729270932	Oct 14, 2022 (156)
48	YY_MCH	ss5809516720	Oct 14, 2022 (156)
49	EVA	ss5830224444	Oct 14, 2022 (156)
50	EVA	ss5848702259	Oct 14, 2022 (156)
51	EVA	ss5856287080	Oct 14, 2022 (156)
52	EVA	ss5888021421	Oct 14, 2022 (156)
53	EVA	ss5974104291	Oct 14, 2022 (156)
54	1000Genomes	NC_000008.10 - 19811024	Oct 12, 2018 (152)
55	1000Genomes_30x	NC_000008.11 - 19953513	Oct 14, 2022 (156)
56	The Avon Longitudinal Study of Parents and Children	NC_000008.10 - 19811024	Oct 12, 2018 (152)
57	Genetic variation in the Estonian population	NC_000008.10 - 19811024	Oct 12, 2018 (152)
58	The Danish reference pan genome	NC_000008.10 - 19811024	Apr 26, 2020 (154)
59	gnomAD - Genomes	NC_000008.11 - 19953513	Apr 27, 2021 (155)
60	Genome of the Netherlands Release 5	NC_000008.10 - 19811024	Apr 26, 2020 (154)
61	Korean Genome Project	NC_000008.11 - 19953513	Apr 26, 2020 (154)
62	Northern Sweden	NC_000008.10 - 19811024	Jul 13, 2019 (153)
63	8.3KJPN	NC_000008.10 - 19811024	Apr 27, 2021 (155)
64	14KJPN	NC_000008.11 - 19953513	Oct 14, 2022 (156)
65	TopMed	NC_000008.11 - 19953513	Apr 27, 2021 (155)
66	UK 10K study - Twins	NC_000008.10 - 19811024	Oct 12, 2018 (152)
67	A Vietnamese Genetic Variation Database	NC_000008.10 - 19811024	Jul 13, 2019 (153)
68	ALFA	NC_000008.11 - 19953513	Apr 27, 2021 (155)
69	ClinVar	RCV001533982.2	Oct 14, 2022 (156)

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)
rs10657763	Oct 08, 2004 (123)
rs57186780	May 15, 2013 (138)
rs142517359	Apr 25, 2013 (138)
rs67369964	Feb 27, 2009 (130)
rs67369965	Feb 27, 2009 (130)
rs67369966	Feb 27, 2009 (130)
rs67369967	Feb 27, 2009 (130)
rs72575590	May 11, 2012 (137)
rs72600711	Feb 27, 2009 (130)
rs144178309	Sep 17, 2011 (135)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss288895653, ss327029962, ss327090017, ss327406283, ss551825305, ss552041870, ss553332751, ss1594862256	NC_000008.9:19855303::TG	NC_000008.11:19953512:TGTGTG:TGTGT… NC_000008.11:19953512:TGTGTG:TGTGTGTG	(self)
ss288895654	NC_000008.9:19855309::TG	NC_000008.11:19953512:TGTGTG:TGTGT… NC_000008.11:19953512:TGTGTG:TGTGTGTG	(self)
41009792, 22797052, 16222685, 1206940, 10186911, 8751884, 45623659, 22797052, 5083454, ss500127589, ss663841921, ss666430660, ss985272595, ss1367861529, ss1577168414, ss1705971022, ss1705971094, ss1805432767, ss2030895904, ss2626975135, ss2986076160, ss3002804408, ss3670484437, ss3735467019, ss3831054889, ss3984393685, ss3986415463, ss5187654352, ss5624176077, ss5644923806, ss5830224444, ss5974104291	NC_000008.10:19811023::TG	NC_000008.11:19953512:TGTGTG:TGTGT… NC_000008.11:19953512:TGTGTG:TGTGTGTG	(self)
ss559644561, ss3984393686, ss3984393687, ss5848702259	NC_000008.10:19811029::TG	NC_000008.11:19953512:TGTGTG:TGTGT… NC_000008.11:19953512:TGTGTG:TGTGTGTG	(self)
53779863, 289194362, 19780130, 63108036, 615469905, ss3066191573, ss3646082947, ss3721555412, ss3810881192, ss3963402129, ss4180332412, ss4778092345, ss5276330108, ss5472980734, ss5566253928, ss5729270932, ss5809516720, ss5856287080, ss5888021421	NC_000008.11:19953512::TG	NC_000008.11:19953512:TGTGTG:TGTGT… NC_000008.11:19953512:TGTGTG:TGTGTGTG	(self)
RCV001533982.2, 13806616769	NC_000008.11:19953512:TGTGTG:TGTGT… NC_000008.11:19953512:TGTGTG:TGTGTGTG	NC_000008.11:19953512:TGTGTG:TGTGT… NC_000008.11:19953512:TGTGTG:TGTGTGTG	(self)
ss2419753	NT_167187.1:7669170::GT	NC_000008.11:19953512:TGTGTG:TGTGT… NC_000008.11:19953512:TGTGTG:TGTGTGTG	(self)
ss82113717	NT_167187.1:7669175::TG	NC_000008.11:19953512:TGTGTG:TGTGT… NC_000008.11:19953512:TGTGTG:TGTGTGTG	(self)
ss193965719	NT_167187.2:7669173::TG	NC_000008.11:19953512:TGTGTG:TGTGT… NC_000008.11:19953512:TGTGTG:TGTGTGTG	(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 rs250

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

rs250