Name: rs57527354
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.

rs57527354

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:30820519 (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: T>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.453500 (120037/264690, TOPMED)
C=0.443889 (62140/139990, GnomAD)
C=0.42164 (13010/30856, ALFA) (+ 18 more)
C=0.47063 (13299/28258, 14KJPN)
C=0.47518 (7964/16760, 8.3KJPN)
C=0.4822 (3088/6404, 1000G_30x)
C=0.4776 (2392/5008, 1000G)
C=0.3540 (1585/4478, Estonian)
C=0.4216 (1625/3854, ALSPAC)
C=0.4129 (1531/3708, TWINSUK)
C=0.4717 (1382/2930, KOREAN)
C=0.4738 (868/1832, Korea1K)
C=0.413 (412/998, GoNL)
C=0.388 (233/600, NorthernSweden)
T=0.352 (148/420, SGDP_PRJ)
T=0.384 (83/216, Qatari)
T=0.500 (107/214, Vietnamese)
C=0.500 (107/214, Vietnamese)
T=0.30 (13/44, Siberian)
C=0.40 (16/40, GENOME_DK)
C=0.24 (8/34, Ancient Sardinia)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: OSBP2 : 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	30856	T=0.57836	C=0.42164
European	Sub	24728	T=0.59766	C=0.40234
African	Sub	3168	T=0.4656	C=0.5344
African Others	Sub	124	T=0.484	C=0.516
African American	Sub	3044	T=0.4648	C=0.5352
Asian	Sub	128	T=0.523	C=0.477
East Asian	Sub	100	T=0.53	C=0.47
Other Asian	Sub	28	T=0.50	C=0.50
Latin American 1	Sub	168	T=0.548	C=0.452
Latin American 2	Sub	700	T=0.593	C=0.407
South Asian	Sub	114	T=0.456	C=0.544
Other	Sub	1850	T=0.5222	C=0.4778

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	T=0.546500	C=0.453500
gnomAD - Genomes	Global	Study-wide	139990	T=0.556111	C=0.443889
gnomAD - Genomes	European	Sub	75840	T=0.60053	C=0.39947
gnomAD - Genomes	African	Sub	41912	T=0.46531	C=0.53469
gnomAD - Genomes	American	Sub	13636	T=0.60186	C=0.39814
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.5340	C=0.4660
gnomAD - Genomes	East Asian	Sub	3126	T=0.5246	C=0.4754
gnomAD - Genomes	Other	Sub	2152	T=0.5493	C=0.4507
Allele Frequency Aggregator	Total	Global	30856	T=0.57836	C=0.42164
Allele Frequency Aggregator	European	Sub	24728	T=0.59766	C=0.40234
Allele Frequency Aggregator	African	Sub	3168	T=0.4656	C=0.5344
Allele Frequency Aggregator	Other	Sub	1850	T=0.5222	C=0.4778
Allele Frequency Aggregator	Latin American 2	Sub	700	T=0.593	C=0.407
Allele Frequency Aggregator	Latin American 1	Sub	168	T=0.548	C=0.452
Allele Frequency Aggregator	Asian	Sub	128	T=0.523	C=0.477
Allele Frequency Aggregator	South Asian	Sub	114	T=0.456	C=0.544
14KJPN	JAPANESE	Study-wide	28258	T=0.52937	C=0.47063
8.3KJPN	JAPANESE	Study-wide	16760	T=0.52482	C=0.47518
1000Genomes_30x	Global	Study-wide	6404	T=0.5178	C=0.4822
1000Genomes_30x	African	Sub	1786	T=0.4446	C=0.5554
1000Genomes_30x	Europe	Sub	1266	T=0.5956	C=0.4044
1000Genomes_30x	South Asian	Sub	1202	T=0.4900	C=0.5100
1000Genomes_30x	East Asian	Sub	1170	T=0.5137	C=0.4863
1000Genomes_30x	American	Sub	980	T=0.590	C=0.410
1000Genomes	Global	Study-wide	5008	T=0.5224	C=0.4776
1000Genomes	African	Sub	1322	T=0.4470	C=0.5530
1000Genomes	East Asian	Sub	1008	T=0.5198	C=0.4802
1000Genomes	Europe	Sub	1006	T=0.6064	C=0.3936
1000Genomes	South Asian	Sub	978	T=0.492	C=0.508
1000Genomes	American	Sub	694	T=0.591	C=0.409
Genetic variation in the Estonian population	Estonian	Study-wide	4478	T=0.6460	C=0.3540
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5784	C=0.4216
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5871	C=0.4129
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.5283	A=0.0000, C=0.4717
Korean Genome Project	KOREAN	Study-wide	1832	T=0.5262	C=0.4738
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.587	C=0.413
Northern Sweden	ACPOP	Study-wide	600	T=0.612	C=0.388
SGDP_PRJ	Global	Study-wide	420	T=0.352	C=0.648
Qatari	Global	Study-wide	216	T=0.384	C=0.616
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.500	C=0.500
Siberian	Global	Study-wide	44	T=0.30	C=0.70
The Danish reference pan genome	Danish	Study-wide	40	T=0.60	C=0.40
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	34	T=0.76	C=0.24

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 22	NC_000022.11:g.30820519T>A
GRCh38.p14 chr 22	NC_000022.11:g.30820519T>C
GRCh37.p13 chr 22	NC_000022.10:g.31216506T>A
GRCh37.p13 chr 22	NC_000022.10:g.31216506T>C

Gene: OSBP2, oxysterol binding protein 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
OSBP2 transcript variant 3	NM_001282738.2:c.359-4991… NM_001282738.2:c.359-49910T>A	N/A	Intron Variant
OSBP2 transcript variant 4	NM_001282739.2:c.854-4991… NM_001282739.2:c.854-49910T>A	N/A	Intron Variant
OSBP2 transcript variant 5	NM_001282740.2:c.-245-499… NM_001282740.2:c.-245-49910T>A	N/A	Intron Variant
OSBP2 transcript variant 1	NM_030758.4:c.854-49910T>A	N/A	Intron Variant
OSBP2 transcript variant 6	NM_001282741.2:c.	N/A	Genic Upstream Transcript Variant
OSBP2 transcript variant 7	NM_001282742.2:c.	N/A	Genic Upstream 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	T=	A	C
GRCh38.p14 chr 22	NC_000022.11:g.30820519=	NC_000022.11:g.30820519T>A	NC_000022.11:g.30820519T>C
GRCh37.p13 chr 22	NC_000022.10:g.31216506=	NC_000022.10:g.31216506T>A	NC_000022.10:g.31216506T>C
OSBP2 transcript variant 3	NM_001282738.2:c.359-49910=	NM_001282738.2:c.359-49910T>A	NM_001282738.2:c.359-49910T>C
OSBP2 transcript variant 4	NM_001282739.2:c.854-49910=	NM_001282739.2:c.854-49910T>A	NM_001282739.2:c.854-49910T>C
OSBP2 transcript variant 5	NM_001282740.2:c.-245-49910=	NM_001282740.2:c.-245-49910T>A	NM_001282740.2:c.-245-49910T>C
OSBP2 transcript variant 1	NM_030758.3:c.854-49910=	NM_030758.3:c.854-49910T>A	NM_030758.3:c.854-49910T>C
OSBP2 transcript variant 1	NM_030758.4:c.854-49910=	NM_030758.4:c.854-49910T>A	NM_030758.4:c.854-49910T>C
OSBP2 transcript variant X1	XM_005261463.1:c.854-49910=	XM_005261463.1:c.854-49910T>A	XM_005261463.1:c.854-49910T>C
OSBP2 transcript variant X2	XM_005261464.1:c.854-49910=	XM_005261464.1:c.854-49910T>A	XM_005261464.1:c.854-49910T>C
OSBP2 transcript variant X3	XM_005261465.1:c.854-49910=	XM_005261465.1:c.854-49910T>A	XM_005261465.1:c.854-49910T>C
OSBP2 transcript variant X4	XM_005261466.1:c.359-49910=	XM_005261466.1:c.359-49910T>A	XM_005261466.1:c.359-49910T>C
OSBP2 transcript variant X6	XM_005261468.1:c.-245-49910=	XM_005261468.1:c.-245-49910T>A	XM_005261468.1:c.-245-49910T>C

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#.

75 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss85837252	Dec 14, 2007 (129)
2	HUMANGENOME_JCVI	ss96121888	Feb 04, 2009 (130)
3	1000GENOMES	ss112609475	Jan 25, 2009 (130)
4	1000GENOMES	ss114141392	Jan 25, 2009 (130)
5	ILLUMINA-UK	ss117389150	Dec 01, 2009 (131)
6	GMI	ss157125207	Dec 01, 2009 (131)
7	COMPLETE_GENOMICS	ss167845120	Jul 04, 2010 (132)
8	COMPLETE_GENOMICS	ss169110956	Jul 04, 2010 (132)
9	COMPLETE_GENOMICS	ss171921274	Jul 04, 2010 (132)
10	BUSHMAN	ss204074885	Jul 04, 2010 (132)
11	1000GENOMES	ss228658330	Jul 14, 2010 (132)
12	1000GENOMES	ss238052557	Jul 15, 2010 (132)
13	1000GENOMES	ss244175511	Jul 15, 2010 (132)
14	GMI	ss283620435	May 04, 2012 (137)
15	GMI	ss287562232	Apr 25, 2013 (138)
16	PJP	ss292752376	May 09, 2011 (134)
17	ILLUMINA	ss483679716	May 04, 2012 (137)
18	ILLUMINA	ss484302521	May 04, 2012 (137)
19	ILLUMINA	ss535882057	Sep 08, 2015 (146)
20	TISHKOFF	ss566611604	Apr 25, 2013 (138)
21	SSMP	ss662542961	Apr 25, 2013 (138)
22	ILLUMINA	ss779423957	Aug 21, 2014 (142)
23	ILLUMINA	ss782283332	Aug 21, 2014 (142)
24	ILLUMINA	ss834893186	Aug 21, 2014 (142)
25	EVA-GONL	ss995307560	Aug 21, 2014 (142)
26	JMKIDD_LAB	ss1082627427	Aug 21, 2014 (142)
27	1000GENOMES	ss1367005263	Aug 21, 2014 (142)
28	DDI	ss1429244397	Apr 01, 2015 (144)
29	EVA_GENOME_DK	ss1579735522	Apr 01, 2015 (144)
30	EVA_UK10K_ALSPAC	ss1639908448	Apr 01, 2015 (144)
31	EVA_UK10K_TWINSUK	ss1682902481	Apr 01, 2015 (144)
32	EVA_DECODE	ss1699377157	Apr 01, 2015 (144)
33	HAMMER_LAB	ss1809770009	Sep 08, 2015 (146)
34	WEILL_CORNELL_DGM	ss1938874017	Feb 12, 2016 (147)
35	GENOMED	ss1969263774	Jul 19, 2016 (147)
36	JJLAB	ss2030208642	Sep 14, 2016 (149)
37	USC_VALOUEV	ss2158825302	Dec 20, 2016 (150)
38	HUMAN_LONGEVITY	ss2247006843	Dec 20, 2016 (150)
39	SYSTEMSBIOZJU	ss2629602855	Nov 08, 2017 (151)
40	ILLUMINA	ss2633872584	Nov 08, 2017 (151)
41	GRF	ss2704576284	Nov 08, 2017 (151)
42	GNOMAD	ss2973933557	Nov 08, 2017 (151)
43	SWEGEN	ss3019236416	Nov 08, 2017 (151)
44	BIOINF_KMB_FNS_UNIBA	ss3028941877	Nov 08, 2017 (151)
45	CSHL	ss3352817822	Nov 08, 2017 (151)
46	ILLUMINA	ss3628524185	Oct 12, 2018 (152)
47	ILLUMINA	ss3631824181	Oct 12, 2018 (152)
48	URBANLAB	ss3651171273	Oct 12, 2018 (152)
49	EGCUT_WGS	ss3685733372	Jul 13, 2019 (153)
50	EVA_DECODE	ss3708117420	Jul 13, 2019 (153)
51	ACPOP	ss3743896573	Jul 13, 2019 (153)
52	EVA	ss3759331868	Jul 13, 2019 (153)
53	KHV_HUMAN_GENOMES	ss3822496300	Jul 13, 2019 (153)
54	EVA	ss3835969413	Apr 27, 2020 (154)
55	EVA	ss3841613046	Apr 27, 2020 (154)
56	EVA	ss3847127894	Apr 27, 2020 (154)
57	SGDP_PRJ	ss3890459311	Apr 27, 2020 (154)
58	KRGDB	ss3940844907	Apr 27, 2020 (154)
59	KOGIC	ss3983559710	Apr 27, 2020 (154)
60	EVA	ss3985915067	Apr 26, 2021 (155)
61	TOPMED	ss5107827673	Apr 26, 2021 (155)
62	TOMMO_GENOMICS	ss5232441405	Apr 26, 2021 (155)
63	1000G_HIGH_COVERAGE	ss5310958470	Oct 16, 2022 (156)
64	EVA	ss5316053434	Oct 16, 2022 (156)
65	EVA	ss5441045119	Oct 16, 2022 (156)
66	HUGCELL_USP	ss5502813416	Oct 16, 2022 (156)
67	EVA	ss5512367531	Oct 16, 2022 (156)
68	1000G_HIGH_COVERAGE	ss5618450373	Oct 16, 2022 (156)
69	SANFORD_IMAGENETICS	ss5664415359	Oct 16, 2022 (156)
70	TOMMO_GENOMICS	ss5793503955	Oct 16, 2022 (156)
71	YY_MCH	ss5818676786	Oct 16, 2022 (156)
72	EVA	ss5822014940	Oct 16, 2022 (156)
73	EVA	ss5853378189	Oct 16, 2022 (156)
74	EVA	ss5881660689	Oct 16, 2022 (156)
75	EVA	ss5959267396	Oct 16, 2022 (156)
76	1000Genomes	NC_000022.10 - 31216506	Oct 12, 2018 (152)
77	1000Genomes_30x	NC_000022.11 - 30820519	Oct 16, 2022 (156)
78	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 31216506	Oct 12, 2018 (152)
79	Genetic variation in the Estonian population	NC_000022.10 - 31216506	Oct 12, 2018 (152)
80	The Danish reference pan genome	NC_000022.10 - 31216506	Apr 27, 2020 (154)
81	gnomAD - Genomes	NC_000022.11 - 30820519	Apr 26, 2021 (155)
82	Genome of the Netherlands Release 5	NC_000022.10 - 31216506	Apr 27, 2020 (154)
83	KOREAN population from KRGDB	NC_000022.10 - 31216506	Apr 27, 2020 (154)
84	Korean Genome Project	NC_000022.11 - 30820519	Apr 27, 2020 (154)
85	Northern Sweden	NC_000022.10 - 31216506	Jul 13, 2019 (153)
86	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000022.10 - 31216506	Apr 26, 2021 (155)
87	Qatari	NC_000022.10 - 31216506	Apr 27, 2020 (154)
88	SGDP_PRJ	NC_000022.10 - 31216506	Apr 27, 2020 (154)
89	Siberian	NC_000022.10 - 31216506	Apr 27, 2020 (154)
90	8.3KJPN	NC_000022.10 - 31216506	Apr 26, 2021 (155)
91	14KJPN	NC_000022.11 - 30820519	Oct 16, 2022 (156)
92	TopMed	NC_000022.11 - 30820519	Apr 26, 2021 (155)
93	UK 10K study - Twins	NC_000022.10 - 31216506	Oct 12, 2018 (152)
94	A Vietnamese Genetic Variation Database	NC_000022.10 - 31216506	Jul 13, 2019 (153)
95	ALFA	NC_000022.11 - 30820519	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
48022301, ss3940844907	NC_000022.10:31216505:T:A	NC_000022.11:30820518:T:A	(self)
ss85837252	NC_000022.8:29541059:T:C	NC_000022.11:30820518:T:C	(self)
ss112609475, ss114141392, ss117389150, ss167845120, ss169110956, ss171921274, ss204074885, ss283620435, ss287562232, ss292752376, ss484302521, ss1699377157	NC_000022.9:29546505:T:C	NC_000022.11:30820518:T:C	(self)
80551312, 44553658, 31471620, 5900461, 19853589, 48022301, 17181438, 1140994, 20915939, 42476291, 11341656, 90410712, 44553658, 9830279, ss228658330, ss238052557, ss244175511, ss483679716, ss535882057, ss566611604, ss662542961, ss779423957, ss782283332, ss834893186, ss995307560, ss1082627427, ss1367005263, ss1429244397, ss1579735522, ss1639908448, ss1682902481, ss1809770009, ss1938874017, ss1969263774, ss2030208642, ss2158825302, ss2629602855, ss2633872584, ss2704576284, ss2973933557, ss3019236416, ss3352817822, ss3628524185, ss3631824181, ss3685733372, ss3743896573, ss3759331868, ss3835969413, ss3841613046, ss3890459311, ss3940844907, ss3985915067, ss5232441405, ss5316053434, ss5441045119, ss5512367531, ss5664415359, ss5822014940, ss5959267396	NC_000022.10:31216505:T:C	NC_000022.11:30820518:T:C	(self)
105976308, 568828346, 39937711, 127341059, 382936620, 9809206027, ss2247006843, ss3028941877, ss3651171273, ss3708117420, ss3822496300, ss3847127894, ss3983559710, ss5107827673, ss5310958470, ss5502813416, ss5618450373, ss5793503955, ss5818676786, ss5853378189, ss5881660689	NC_000022.11:30820518:T:C	NC_000022.11:30820518:T:C	(self)
ss96121888, ss157125207	NT_011520.12:10607074:T:C	NC_000022.11:30820518:T:C	(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 rs57527354

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

rs57527354