Name: rs254
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.

rs254

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr8:19954386 (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: C>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.182338 (48263/264690, TOPMED)
G=0.166996 (41423/248048, GnomAD_exome)
G=0.175960 (24647/140072, GnomAD) (+ 21 more)
G=0.170677 (20130/117942, ExAC)
G=0.22054 (6232/28258, 14KJPN)
G=0.16568 (4631/27952, ALFA)
G=0.22321 (3741/16760, 8.3KJPN)
G=0.10349 (1346/13006, GO-ESP)
G=0.2116 (1355/6404, 1000G_30x)
G=0.2067 (1035/5008, 1000G)
G=0.1404 (629/4480, Estonian)
G=0.1510 (582/3854, ALSPAC)
G=0.1502 (557/3708, TWINSUK)
G=0.2099 (615/2930, KOREAN)
G=0.1943 (356/1832, Korea1K)
G=0.141 (141/998, GoNL)
G=0.115 (69/600, NorthernSweden)
G=0.167 (89/534, MGP)
G=0.153 (33/216, Qatari)
C=0.413 (81/196, SGDP_PRJ)
G=0.000 (0/114, HapMap)
G=0.15 (6/40, GENOME_DK)
C=0.50 (8/16, Siberian)
G=0.50 (8/16, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: LPL : Intron Variant
Publications: 1 citation
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	27952	C=0.83432	G=0.16568	0.699485	0.030839	0.269677	5
European	Sub	20398	C=0.84881	G=0.15119	0.72311	0.025493	0.251397	3
African	Sub	3554	C=0.7665	G=0.2335	0.593697	0.060777	0.345526	1
African Others	Sub	122	C=0.770	G=0.230	0.622951	0.081967	0.295082	1
African American	Sub	3432	C=0.7663	G=0.2337	0.592657	0.060023	0.347319	1
Asian	Sub	168	C=0.726	G=0.274	0.5	0.047619	0.452381	1
East Asian	Sub	112	C=0.705	G=0.295	0.482143	0.071429	0.446429	0
Other Asian	Sub	56	C=0.77	G=0.23	0.535714	0.0	0.464286	2
Latin American 1	Sub	146	C=0.877	G=0.123	0.767123	0.013699	0.219178	0
Latin American 2	Sub	610	C=0.836	G=0.164	0.708197	0.036066	0.255738	1
South Asian	Sub	98	C=0.77	G=0.23	0.612245	0.081633	0.306122	1
Other	Sub	2978	C=0.8220	G=0.1780	0.672935	0.028878	0.298187	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	C=0.817662	G=0.182338
gnomAD - Exomes	Global	Study-wide	248048	C=0.833004	G=0.166996
gnomAD - Exomes	European	Sub	132898	C=0.861059	G=0.138941
gnomAD - Exomes	Asian	Sub	48654	C=0.77708	G=0.22292
gnomAD - Exomes	American	Sub	34278	C=0.84279	G=0.15721
gnomAD - Exomes	African	Sub	16124	C=0.76414	G=0.23586
gnomAD - Exomes	Ashkenazi Jewish	Sub	10018	C=0.80505	G=0.19495
gnomAD - Exomes	Other	Sub	6076	C=0.8408	G=0.1592
gnomAD - Genomes	Global	Study-wide	140072	C=0.824040	G=0.175960
gnomAD - Genomes	European	Sub	75898	C=0.85594	G=0.14406
gnomAD - Genomes	African	Sub	41920	C=0.76999	G=0.23001
gnomAD - Genomes	American	Sub	13654	C=0.82408	G=0.17592
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.8064	G=0.1936
gnomAD - Genomes	East Asian	Sub	3126	C=0.7866	G=0.2134
gnomAD - Genomes	Other	Sub	2152	C=0.8332	G=0.1668
ExAC	Global	Study-wide	117942	C=0.829323	G=0.170677
ExAC	Europe	Sub	71332	C=0.85511	G=0.14489
ExAC	Asian	Sub	24506	C=0.77348	G=0.22652
ExAC	American	Sub	11062	C=0.84153	G=0.15847
ExAC	African	Sub	10152	C=0.76714	G=0.23286
ExAC	Other	Sub	890	C=0.857	G=0.143
14KJPN	JAPANESE	Study-wide	28258	C=0.77946	G=0.22054
Allele Frequency Aggregator	Total	Global	27952	C=0.83432	G=0.16568
Allele Frequency Aggregator	European	Sub	20398	C=0.84881	G=0.15119
Allele Frequency Aggregator	African	Sub	3554	C=0.7665	G=0.2335
Allele Frequency Aggregator	Other	Sub	2978	C=0.8220	G=0.1780
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.836	G=0.164
Allele Frequency Aggregator	Asian	Sub	168	C=0.726	G=0.274
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.877	G=0.123
Allele Frequency Aggregator	South Asian	Sub	98	C=0.77	G=0.23
8.3KJPN	JAPANESE	Study-wide	16760	C=0.77679	G=0.22321
GO Exome Sequencing Project	Global	Study-wide	13006	C=0.89651	G=0.10349
GO Exome Sequencing Project	European American	Sub	8600	C=0.9210	G=0.0790
GO Exome Sequencing Project	African American	Sub	4406	C=0.8486	G=0.1514
1000Genomes_30x	Global	Study-wide	6404	C=0.7884	G=0.2116
1000Genomes_30x	African	Sub	1786	C=0.7732	G=0.2268
1000Genomes_30x	Europe	Sub	1266	C=0.8325	G=0.1675
1000Genomes_30x	South Asian	Sub	1202	C=0.7671	G=0.2329
1000Genomes_30x	East Asian	Sub	1170	C=0.7487	G=0.2513
1000Genomes_30x	American	Sub	980	C=0.833	G=0.167
1000Genomes	Global	Study-wide	5008	C=0.7933	G=0.2067
1000Genomes	African	Sub	1322	C=0.7806	G=0.2194
1000Genomes	East Asian	Sub	1008	C=0.7520	G=0.2480
1000Genomes	Europe	Sub	1006	C=0.8479	G=0.1521
1000Genomes	South Asian	Sub	978	C=0.764	G=0.236
1000Genomes	American	Sub	694	C=0.840	G=0.160
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8596	G=0.1404
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8490	G=0.1510
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8498	G=0.1502
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.7901	G=0.2099
Korean Genome Project	KOREAN	Study-wide	1832	C=0.8057	G=0.1943
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.859	G=0.141
Northern Sweden	ACPOP	Study-wide	600	C=0.885	G=0.115
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.833	G=0.167
Qatari	Global	Study-wide	216	C=0.847	G=0.153
SGDP_PRJ	Global	Study-wide	196	C=0.413	G=0.587
HapMap	Global	Study-wide	114	C=1.000	G=0.000
HapMap	American	Sub	114	C=1.000	G=0.000
The Danish reference pan genome	Danish	Study-wide	40	C=0.85	G=0.15
Siberian	Global	Study-wide	16	C=0.50	G=0.50

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.19954386C>G
GRCh37.p13 chr 8	NC_000008.10:g.19811897C>G
LPL RefSeqGene (LRG_1298)	NG_008855.2:g.57670C>G

Gene: LPL, lipoprotein lipase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LPL transcript	NM_000237.3:c.775+33C>G	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: G (allele ID: 1233959 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001644086.2	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	C=	G
GRCh38.p14 chr 8	NC_000008.11:g.19954386=	NC_000008.11:g.19954386C>G
GRCh37.p13 chr 8	NC_000008.10:g.19811897=	NC_000008.10:g.19811897C>G
LPL RefSeqGene (LRG_1298)	NG_008855.2:g.57670=	NG_008855.2:g.57670C>G
LPL transcript	NM_000237.2:c.775+33=	NM_000237.2:c.775+33C>G
LPL transcript	NM_000237.3:c.775+33=	NM_000237.3:c.775+33C>G

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#.

76 SubSNP, 23 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	DEBNICK	ss254	Sep 19, 2000 (36)
2	WI_SSAHASNP	ss6803992	Feb 20, 2003 (111)
3	BCM_SSAHASNP	ss10448011	Jul 11, 2003 (116)
4	IMCJ-GDT	ss16343009	Feb 27, 2004 (120)
5	BGI	ss104512503	Dec 01, 2009 (131)
6	COMPLETE_GENOMICS	ss162223987	Jul 04, 2010 (132)
7	BUSHMAN	ss198888079	Jul 04, 2010 (132)
8	1000GENOMES	ss223585620	Jul 14, 2010 (132)
9	1000GENOMES	ss234352464	Jul 15, 2010 (132)
10	1000GENOMES	ss241227288	Jul 15, 2010 (132)
11	BL	ss254171393	May 09, 2011 (134)
12	GMI	ss279724009	May 04, 2012 (137)
13	ILLUMINA	ss410878526	Sep 17, 2011 (135)
14	1000GENOMES	ss490960916	May 04, 2012 (137)
15	ILLUMINA	ss532825739	Sep 08, 2015 (146)
16	TISHKOFF	ss560600100	Apr 25, 2013 (138)
17	SSMP	ss655035538	Apr 25, 2013 (138)
18	NHLBI-ESP	ss712828525	Apr 25, 2013 (138)
19	EVA-GONL	ss985272605	Aug 21, 2014 (142)
20	JMKIDD_LAB	ss1075339990	Aug 21, 2014 (142)
21	1000GENOMES	ss1328915081	Aug 21, 2014 (142)
22	DDI	ss1431441571	Apr 01, 2015 (144)
23	EVA_GENOME_DK	ss1582593745	Apr 01, 2015 (144)
24	EVA_DECODE	ss1594862261	Apr 01, 2015 (144)
25	EVA_UK10K_ALSPAC	ss1620133674	Apr 01, 2015 (144)
26	EVA_UK10K_TWINSUK	ss1663127707	Apr 01, 2015 (144)
27	EVA_EXAC	ss1689111530	Apr 01, 2015 (144)
28	EVA_MGP	ss1711194697	Apr 01, 2015 (144)
29	HAMMER_LAB	ss1805432773	Sep 08, 2015 (146)
30	WEILL_CORNELL_DGM	ss1928562353	Feb 12, 2016 (147)
31	GENOMED	ss1970929927	Jul 19, 2016 (147)
32	JJLAB	ss2024980538	Sep 14, 2016 (149)
33	USC_VALOUEV	ss2153202004	Dec 20, 2016 (150)
34	HUMAN_LONGEVITY	ss2301287825	Dec 20, 2016 (150)
35	SYSTEMSBIOZJU	ss2626975139	Nov 08, 2017 (151)
36	GRF	ss2708962513	Nov 08, 2017 (151)
37	GNOMAD	ss2737022321	Nov 08, 2017 (151)
38	GNOMAD	ss2748007706	Nov 08, 2017 (151)
39	GNOMAD	ss2864092718	Nov 08, 2017 (151)
40	SWEGEN	ss3002804419	Nov 08, 2017 (151)
41	BIOINF_KMB_FNS_UNIBA	ss3026281094	Nov 08, 2017 (151)
42	CSHL	ss3348082017	Nov 08, 2017 (151)
43	ILLUMINA	ss3630013631	Oct 12, 2018 (152)
44	OMUKHERJEE_ADBS	ss3646373015	Oct 12, 2018 (152)
45	EGCUT_WGS	ss3670484444	Jul 13, 2019 (153)
46	EVA_DECODE	ss3721555420	Jul 13, 2019 (153)
47	ACPOP	ss3735467022	Jul 13, 2019 (153)
48	EVA	ss3767717740	Jul 13, 2019 (153)
49	PACBIO	ss3786087356	Jul 13, 2019 (153)
50	PACBIO	ss3791353765	Jul 13, 2019 (153)
51	PACBIO	ss3796234932	Jul 13, 2019 (153)
52	KHV_HUMAN_GENOMES	ss3810881201	Jul 13, 2019 (153)
53	EVA	ss3824351396	Apr 26, 2020 (154)
54	EVA	ss3825737071	Apr 26, 2020 (154)
55	EVA	ss3831054893	Apr 26, 2020 (154)
56	SGDP_PRJ	ss3869436687	Apr 26, 2020 (154)
57	KRGDB	ss3916862518	Apr 26, 2020 (154)
58	KOGIC	ss3963402152	Apr 26, 2020 (154)
59	FSA-LAB	ss3984393688	Apr 27, 2021 (155)
60	FSA-LAB	ss3984393689	Apr 27, 2021 (155)
61	EVA	ss3986415469	Apr 27, 2021 (155)
62	TOPMED	ss4778092588	Apr 27, 2021 (155)
63	TOMMO_GENOMICS	ss5187654381	Apr 27, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5276330125	Oct 14, 2022 (156)
65	HUGCELL_USP	ss5472980747	Oct 14, 2022 (156)
66	EVA	ss5509275465	Oct 14, 2022 (156)
67	1000G_HIGH_COVERAGE	ss5566253964	Oct 14, 2022 (156)
68	EVA	ss5624176078	Oct 14, 2022 (156)
69	SANFORD_IMAGENETICS	ss5644923816	Oct 14, 2022 (156)
70	TOMMO_GENOMICS	ss5729270969	Oct 14, 2022 (156)
71	YY_MCH	ss5809516726	Oct 14, 2022 (156)
72	EVA	ss5830224450	Oct 14, 2022 (156)
73	EVA	ss5848702260	Oct 14, 2022 (156)
74	EVA	ss5856287084	Oct 14, 2022 (156)
75	EVA	ss5888021453	Oct 14, 2022 (156)
76	EVA	ss5974104307	Oct 14, 2022 (156)
77	1000Genomes	NC_000008.10 - 19811897	Oct 12, 2018 (152)
78	1000Genomes_30x	NC_000008.11 - 19954386	Oct 14, 2022 (156)
79	The Avon Longitudinal Study of Parents and Children	NC_000008.10 - 19811897	Oct 12, 2018 (152)
80	Genetic variation in the Estonian population	NC_000008.10 - 19811897	Oct 12, 2018 (152)
81	ExAC	NC_000008.10 - 19811897	Oct 12, 2018 (152)
82	The Danish reference pan genome	NC_000008.10 - 19811897	Apr 26, 2020 (154)
83	gnomAD - Genomes	NC_000008.11 - 19954386	Apr 27, 2021 (155)
84	gnomAD - Exomes	NC_000008.10 - 19811897	Jul 13, 2019 (153)
85	GO Exome Sequencing Project	NC_000008.10 - 19811897	Oct 12, 2018 (152)
86	Genome of the Netherlands Release 5	NC_000008.10 - 19811897	Apr 26, 2020 (154)
87	HapMap	NC_000008.11 - 19954386	Apr 26, 2020 (154)
88	KOREAN population from KRGDB	NC_000008.10 - 19811897	Apr 26, 2020 (154)
89	Korean Genome Project	NC_000008.11 - 19954386	Apr 26, 2020 (154)
90	Medical Genome Project healthy controls from Spanish population	NC_000008.10 - 19811897	Apr 26, 2020 (154)
91	Northern Sweden	NC_000008.10 - 19811897	Jul 13, 2019 (153)
92	Qatari	NC_000008.10 - 19811897	Apr 26, 2020 (154)
93	SGDP_PRJ	NC_000008.10 - 19811897	Apr 26, 2020 (154)
94	Siberian	NC_000008.10 - 19811897	Apr 26, 2020 (154)
95	8.3KJPN	NC_000008.10 - 19811897	Apr 27, 2021 (155)
96	14KJPN	NC_000008.11 - 19954386	Oct 14, 2022 (156)
97	TopMed	NC_000008.11 - 19954386	Apr 27, 2021 (155)
98	UK 10K study - Twins	NC_000008.10 - 19811897	Oct 12, 2018 (152)
99	ALFA	NC_000008.11 - 19954386	Apr 27, 2021 (155)
100	ClinVar	RCV001644086.2	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss162223987, ss198888079, ss254171393, ss279724009, ss410878526, ss1594862261	NC_000008.9:19856176:C:G	NC_000008.11:19954385:C:G	(self)
41009823, 22797066, 16222692, 9205123, 8758683, 6190704, 809248, 10186921, 24039912, 310457, 8751887, 10604283, 21453667, 5718358, 45623688, 22797066, ss223585620, ss234352464, ss241227288, ss490960916, ss532825739, ss560600100, ss655035538, ss712828525, ss985272605, ss1075339990, ss1328915081, ss1431441571, ss1582593745, ss1620133674, ss1663127707, ss1689111530, ss1711194697, ss1805432773, ss1928562353, ss1970929927, ss2024980538, ss2153202004, ss2626975139, ss2708962513, ss2737022321, ss2748007706, ss2864092718, ss3002804419, ss3348082017, ss3630013631, ss3646373015, ss3670484444, ss3735467022, ss3767717740, ss3786087356, ss3791353765, ss3796234932, ss3824351396, ss3825737071, ss3831054893, ss3869436687, ss3916862518, ss3984393688, ss3984393689, ss3986415469, ss5187654381, ss5509275465, ss5624176078, ss5644923816, ss5830224450, ss5848702260, ss5974104307	NC_000008.10:19811896:C:G	NC_000008.11:19954385:C:G	(self)
RCV001644086.2, 53779899, 289194547, 3580968, 19780153, 63108073, 615470148, 4578013581, ss2301287825, ss3026281094, ss3721555420, ss3810881201, ss3963402152, ss4778092588, ss5276330125, ss5472980747, ss5566253964, ss5729270969, ss5809516726, ss5856287084, ss5888021453	NC_000008.11:19954385:C:G	NC_000008.11:19954385:C:G	(self)
ss10448011	NT_030737.7:3533120:C:G	NC_000008.11:19954385:C:G	(self)
ss254, ss6803992, ss16343009, ss104512503	NT_167187.1:7670042:C:G	NC_000008.11:19954385:C:G	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs254

PMID	Title	Author	Year	Journal
24491308	Systematic review and meta-analysis of candidate gene association studies of lower urinary tract symptoms in men.	Cartwright R et al.	2014	European urology

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

rs254