Name: rs5753357
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.

rs5753357

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:30865367 (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: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.223775 (59231/264690, TOPMED)
G=0.230080 (32220/140038, GnomAD)
G=0.43336 (12246/28258, 14KJPN) (+ 16 more)
G=0.26818 (5066/18890, ALFA)
G=0.43109 (7225/16760, 8.3KJPN)
G=0.2637 (1689/6404, 1000G_30x)
G=0.2702 (1353/5008, 1000G)
G=0.3935 (1763/4480, Estonian)
G=0.2501 (964/3854, ALSPAC)
G=0.2602 (965/3708, TWINSUK)
G=0.4031 (1181/2930, KOREAN)
G=0.4099 (751/1832, Korea1K)
G=0.271 (270/998, GoNL)
G=0.283 (170/600, NorthernSweden)
A=0.414 (110/266, SGDP_PRJ)
G=0.167 (36/216, Qatari)
G=0.330 (70/212, Vietnamese)
G=0.33 (13/40, GENOME_DK)
A=0.45 (17/38, Siberian)

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	18890	A=0.73182	G=0.26818
European	Sub	14286	A=0.70286	G=0.29714
African	Sub	2946	A=0.8734	G=0.1266
African Others	Sub	114	A=0.930	G=0.070
African American	Sub	2832	A=0.8711	G=0.1289
Asian	Sub	112	A=0.589	G=0.411
East Asian	Sub	86	A=0.59	G=0.41
Other Asian	Sub	26	A=0.58	G=0.42
Latin American 1	Sub	146	A=0.815	G=0.185
Latin American 2	Sub	610	A=0.721	G=0.279
South Asian	Sub	98	A=0.61	G=0.39
Other	Sub	692	A=0.759	G=0.241

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	A=0.776225	G=0.223775
gnomAD - Genomes	Global	Study-wide	140038	A=0.769920	G=0.230080
gnomAD - Genomes	European	Sub	75816	A=0.71786	G=0.28214
gnomAD - Genomes	African	Sub	41994	A=0.87505	G=0.12495
gnomAD - Genomes	American	Sub	13632	A=0.77267	G=0.22733
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	A=0.7858	G=0.2142
gnomAD - Genomes	East Asian	Sub	3126	A=0.5889	G=0.4111
gnomAD - Genomes	Other	Sub	2150	A=0.7735	G=0.2265
14KJPN	JAPANESE	Study-wide	28258	A=0.56664	G=0.43336
Allele Frequency Aggregator	Total	Global	18890	A=0.73182	G=0.26818
Allele Frequency Aggregator	European	Sub	14286	A=0.70286	G=0.29714
Allele Frequency Aggregator	African	Sub	2946	A=0.8734	G=0.1266
Allele Frequency Aggregator	Other	Sub	692	A=0.759	G=0.241
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.721	G=0.279
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.815	G=0.185
Allele Frequency Aggregator	Asian	Sub	112	A=0.589	G=0.411
Allele Frequency Aggregator	South Asian	Sub	98	A=0.61	G=0.39
8.3KJPN	JAPANESE	Study-wide	16760	A=0.56891	G=0.43109
1000Genomes_30x	Global	Study-wide	6404	A=0.7363	G=0.2637
1000Genomes_30x	African	Sub	1786	A=0.9267	G=0.0733
1000Genomes_30x	Europe	Sub	1266	A=0.7354	G=0.2646
1000Genomes_30x	South Asian	Sub	1202	A=0.5799	G=0.4201
1000Genomes_30x	East Asian	Sub	1170	A=0.6094	G=0.3906
1000Genomes_30x	American	Sub	980	A=0.734	G=0.266
1000Genomes	Global	Study-wide	5008	A=0.7298	G=0.2702
1000Genomes	African	Sub	1322	A=0.9221	G=0.0779
1000Genomes	East Asian	Sub	1008	A=0.6062	G=0.3938
1000Genomes	Europe	Sub	1006	A=0.7455	G=0.2545
1000Genomes	South Asian	Sub	978	A=0.578	G=0.422
1000Genomes	American	Sub	694	A=0.735	G=0.265
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.6065	G=0.3935
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.7499	G=0.2501
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.7398	G=0.2602
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.5969	G=0.4031
Korean Genome Project	KOREAN	Study-wide	1832	A=0.5901	G=0.4099
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.729	G=0.271
Northern Sweden	ACPOP	Study-wide	600	A=0.717	G=0.283
SGDP_PRJ	Global	Study-wide	266	A=0.414	G=0.586
Qatari	Global	Study-wide	216	A=0.833	G=0.167
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.670	G=0.330
The Danish reference pan genome	Danish	Study-wide	40	A=0.68	G=0.33
Siberian	Global	Study-wide	38	A=0.45	G=0.55

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.30865367A>G
GRCh37.p13 chr 22	NC_000022.10:g.31261354A>G

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

Molecule type	Change	Amino acid[Codon]	SO Term
OSBP2 transcript variant 3	NM_001282738.2:c.359-5062… NM_001282738.2:c.359-5062A>G	N/A	Intron Variant
OSBP2 transcript variant 4	NM_001282739.2:c.854-5062… NM_001282739.2:c.854-5062A>G	N/A	Intron Variant
OSBP2 transcript variant 5	NM_001282740.2:c.-245-506… NM_001282740.2:c.-245-5062A>G	N/A	Intron Variant
OSBP2 transcript variant 6	NM_001282741.2:c.80-5062A… NM_001282741.2:c.80-5062A>G	N/A	Intron Variant
OSBP2 transcript variant 1	NM_030758.4:c.854-5062A>G	N/A	Intron 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	A=	G
GRCh38.p14 chr 22	NC_000022.11:g.30865367=	NC_000022.11:g.30865367A>G
GRCh37.p13 chr 22	NC_000022.10:g.31261354=	NC_000022.10:g.31261354A>G
OSBP2 transcript variant 3	NM_001282738.2:c.359-5062=	NM_001282738.2:c.359-5062A>G
OSBP2 transcript variant 4	NM_001282739.2:c.854-5062=	NM_001282739.2:c.854-5062A>G
OSBP2 transcript variant 5	NM_001282740.2:c.-245-5062=	NM_001282740.2:c.-245-5062A>G
OSBP2 transcript variant 6	NM_001282741.2:c.80-5062=	NM_001282741.2:c.80-5062A>G
OSBP2 transcript variant 1	NM_030758.3:c.854-5062=	NM_030758.3:c.854-5062A>G
OSBP2 transcript variant 1	NM_030758.4:c.854-5062=	NM_030758.4:c.854-5062A>G
OSBP2 transcript variant X1	XM_005261463.1:c.854-5062=	XM_005261463.1:c.854-5062A>G
OSBP2 transcript variant X2	XM_005261464.1:c.854-5062=	XM_005261464.1:c.854-5062A>G
OSBP2 transcript variant X3	XM_005261465.1:c.854-5062=	XM_005261465.1:c.854-5062A>G
OSBP2 transcript variant X4	XM_005261466.1:c.359-5062=	XM_005261466.1:c.359-5062A>G
OSBP2 transcript variant X5	XM_005261467.1:c.80-5062=	XM_005261467.1:c.80-5062A>G
OSBP2 transcript variant X6	XM_005261468.1:c.-245-5062=	XM_005261468.1:c.-245-5062A>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#.

56 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8002471	Apr 21, 2003 (114)
2	SC_SNP	ss13354859	Dec 05, 2003 (119)
3	HGSV	ss86145167	Dec 15, 2007 (130)
4	GMI	ss157125550	Dec 01, 2009 (131)
5	COMPLETE_GENOMICS	ss167845462	Jul 04, 2010 (132)
6	COMPLETE_GENOMICS	ss171921467	Jul 04, 2010 (132)
7	BUSHMAN	ss204074974	Jul 04, 2010 (132)
8	GMI	ss283620564	May 04, 2012 (137)
9	1000GENOMES	ss341142964	May 09, 2011 (134)
10	TISHKOFF	ss566611806	Apr 25, 2013 (138)
11	SSMP	ss662543150	Apr 25, 2013 (138)
12	EVA-GONL	ss995307874	Aug 21, 2014 (142)
13	JMKIDD_LAB	ss1082627630	Aug 21, 2014 (142)
14	1000GENOMES	ss1367006410	Aug 21, 2014 (142)
15	DDI	ss1429244470	Apr 01, 2015 (144)
16	EVA_GENOME_DK	ss1579735643	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1639909142	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1682903175	Apr 01, 2015 (144)
19	EVA_DECODE	ss1699377512	Apr 01, 2015 (144)
20	HAMMER_LAB	ss1809770132	Sep 08, 2015 (146)
21	WEILL_CORNELL_DGM	ss1938874321	Feb 12, 2016 (147)
22	GENOMED	ss1969263835	Jul 19, 2016 (147)
23	JJLAB	ss2030208811	Sep 14, 2016 (149)
24	USC_VALOUEV	ss2158825476	Dec 20, 2016 (150)
25	HUMAN_LONGEVITY	ss2247009377	Dec 20, 2016 (150)
26	SYSTEMSBIOZJU	ss2629602946	Nov 08, 2017 (151)
27	GRF	ss2704576483	Nov 08, 2017 (151)
28	GNOMAD	ss2973937022	Nov 08, 2017 (151)
29	SWEGEN	ss3019236978	Nov 08, 2017 (151)
30	BIOINF_KMB_FNS_UNIBA	ss3028941975	Nov 08, 2017 (151)
31	CSHL	ss3352817963	Nov 08, 2017 (151)
32	EGCUT_WGS	ss3685733928	Jul 13, 2019 (153)
33	EVA_DECODE	ss3708118047	Jul 13, 2019 (153)
34	ACPOP	ss3743896861	Jul 13, 2019 (153)
35	EVA	ss3759332236	Jul 13, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3822496684	Jul 13, 2019 (153)
37	EVA	ss3835969554	Apr 27, 2020 (154)
38	EVA	ss3841613129	Apr 27, 2020 (154)
39	EVA	ss3847127979	Apr 27, 2020 (154)
40	SGDP_PRJ	ss3890459942	Apr 27, 2020 (154)
41	KRGDB	ss3940845659	Apr 27, 2020 (154)
42	KOGIC	ss3983560387	Apr 27, 2020 (154)
43	TOPMED	ss5107838549	Apr 26, 2021 (155)
44	TOMMO_GENOMICS	ss5232442805	Apr 26, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5310959549	Oct 16, 2022 (156)
46	EVA	ss5441047074	Oct 16, 2022 (156)
47	HUGCELL_USP	ss5502814393	Oct 16, 2022 (156)
48	EVA	ss5512367654	Oct 16, 2022 (156)
49	1000G_HIGH_COVERAGE	ss5618451920	Oct 16, 2022 (156)
50	SANFORD_IMAGENETICS	ss5664415906	Oct 16, 2022 (156)
51	TOMMO_GENOMICS	ss5793505813	Oct 16, 2022 (156)
52	YY_MCH	ss5818677071	Oct 16, 2022 (156)
53	EVA	ss5822015383	Oct 16, 2022 (156)
54	EVA	ss5853378319	Oct 16, 2022 (156)
55	EVA	ss5881661840	Oct 16, 2022 (156)
56	EVA	ss5959267999	Oct 16, 2022 (156)
57	1000Genomes	NC_000022.10 - 31261354	Oct 12, 2018 (152)
58	1000Genomes_30x	NC_000022.11 - 30865367	Oct 16, 2022 (156)
59	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 31261354	Oct 12, 2018 (152)
60	Genetic variation in the Estonian population	NC_000022.10 - 31261354	Oct 12, 2018 (152)
61	The Danish reference pan genome	NC_000022.10 - 31261354	Apr 27, 2020 (154)
62	gnomAD - Genomes	NC_000022.11 - 30865367	Apr 26, 2021 (155)
63	Genome of the Netherlands Release 5	NC_000022.10 - 31261354	Apr 27, 2020 (154)
64	KOREAN population from KRGDB	NC_000022.10 - 31261354	Apr 27, 2020 (154)
65	Korean Genome Project	NC_000022.11 - 30865367	Apr 27, 2020 (154)
66	Northern Sweden	NC_000022.10 - 31261354	Jul 13, 2019 (153)
67	Qatari	NC_000022.10 - 31261354	Apr 27, 2020 (154)
68	SGDP_PRJ	NC_000022.10 - 31261354	Apr 27, 2020 (154)
69	Siberian	NC_000022.10 - 31261354	Apr 27, 2020 (154)
70	8.3KJPN	NC_000022.10 - 31261354	Apr 26, 2021 (155)
71	14KJPN	NC_000022.11 - 30865367	Oct 16, 2022 (156)
72	TopMed	NC_000022.11 - 30865367	Apr 26, 2021 (155)
73	UK 10K study - Twins	NC_000022.10 - 31261354	Oct 12, 2018 (152)
74	A Vietnamese Genetic Variation Database	NC_000022.10 - 31261354	Jul 13, 2019 (153)
75	ALFA	NC_000022.11 - 30865367	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)
rs58987560	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss86145167	NC_000022.8:29585907:A:G	NC_000022.11:30865366:A:G	(self)
ss167845462, ss171921467, ss204074974, ss283620564, ss1699377512	NC_000022.9:29591353:A:G	NC_000022.11:30865366:A:G	(self)
80552505, 44554424, 31472176, 5900582, 19853879, 48023053, 17181726, 20916243, 42476922, 11341830, 90412112, 44554424, 9830444, ss341142964, ss566611806, ss662543150, ss995307874, ss1082627630, ss1367006410, ss1429244470, ss1579735643, ss1639909142, ss1682903175, ss1809770132, ss1938874321, ss1969263835, ss2030208811, ss2158825476, ss2629602946, ss2704576483, ss2973937022, ss3019236978, ss3352817963, ss3685733928, ss3743896861, ss3759332236, ss3835969554, ss3841613129, ss3890459942, ss3940845659, ss5232442805, ss5441047074, ss5512367654, ss5664415906, ss5822015383, ss5959267999	NC_000022.10:31261353:A:G	NC_000022.11:30865366:A:G	(self)
105977855, 568837218, 39938388, 127342917, 382947496, 12580232072, ss2247009377, ss3028941975, ss3708118047, ss3822496684, ss3847127979, ss3983560387, ss5107838549, ss5310959549, ss5502814393, ss5618451920, ss5793505813, ss5818677071, ss5853378319, ss5881661840	NC_000022.11:30865366:A:G	NC_000022.11:30865366:A:G	(self)
ss13354859	NT_011520.9:10651922:A:G	NC_000022.11:30865366:A:G	(self)
ss8002471, ss157125550	NT_011520.12:10651922:A:G	NC_000022.11:30865366:A:G	(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 rs5753357

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

rs5753357