Name: rs59502379
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.

rs59502379

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:21205999 (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: G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.011387 (3014/264690, TOPMED)
C=0.002591 (650/250838, GnomAD_exome)
C=0.011047 (1546/139952, GnomAD) (+ 11 more)
C=0.003196 (387/121070, ExAC)
C=0.001452 (160/110176, ALFA)
C=0.01672 (1316/78694, PAGE_STUDY)
C=0.01200 (156/13004, GO-ESP)
C=0.0117 (75/6404, 1000G_30x)
C=0.0112 (56/5008, 1000G)
C=0.0012 (4/3300, PRJNA289433)
C=0.002 (1/534, MGP)
C=0.023 (8/350, PharmGKB)
C=0.005 (1/216, Qatari)
G=0.3 (3/10, SGDP_PRJ)

Clinical Significance: Reported in ClinVar
Gene : Consequence: SLCO1B1 : Missense Variant
Publications: 6 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	110176	G=0.998548	C=0.001452	0.997132	3.6e-05	0.002832	17
European	Sub	92452	G=0.99999	C=0.00001	0.999978	0.0	0.000022	0
African	Sub	4360	G=0.9683	C=0.0317	0.937615	0.000917	0.061468	0
African Others	Sub	174	G=0.954	C=0.046	0.908046	0.0	0.091954	0
African American	Sub	4186	G=0.9689	C=0.0311	0.938844	0.000956	0.060201	0
Asian	Sub	3330	G=1.0000	C=0.0000	1.0	0.0	0.0	N/A
East Asian	Sub	2674	G=1.0000	C=0.0000	1.0	0.0	0.0	N/A
Other Asian	Sub	656	G=1.000	C=0.000	1.0	0.0	0.0	N/A
Latin American 1	Sub	790	G=0.992	C=0.008	0.98481	0.0	0.01519	0
Latin American 2	Sub	946	G=0.998	C=0.002	0.995772	0.0	0.004228	0
South Asian	Sub	274	G=1.000	C=0.000	1.0	0.0	0.0	N/A
Other	Sub	8024	G=0.9984	C=0.0016	0.99676	0.0	0.00324	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	G=0.988613	C=0.011387
gnomAD - Exomes	Global	Study-wide	250838	G=0.997409	C=0.002591
gnomAD - Exomes	European	Sub	135050	G=0.999970	C=0.000030
gnomAD - Exomes	Asian	Sub	48952	G=1.00000	C=0.00000
gnomAD - Exomes	American	Sub	34454	G=0.99855	C=0.00145
gnomAD - Exomes	African	Sub	16222	G=0.96369	C=0.03631
gnomAD - Exomes	Ashkenazi Jewish	Sub	10042	G=1.00000	C=0.00000
gnomAD - Exomes	Other	Sub	6118	G=0.9989	C=0.0011
gnomAD - Genomes	Global	Study-wide	139952	G=0.988953	C=0.011047
gnomAD - Genomes	European	Sub	75802	G=0.99989	C=0.00011
gnomAD - Genomes	African	Sub	41974	G=0.96484	C=0.03516
gnomAD - Genomes	American	Sub	13584	G=0.99639	C=0.00361
gnomAD - Genomes	Ashkenazi Jewish	Sub	3314	G=1.0000	C=0.0000
gnomAD - Genomes	East Asian	Sub	3130	G=1.0000	C=0.0000
gnomAD - Genomes	Other	Sub	2148	G=0.9939	C=0.0061
ExAC	Global	Study-wide	121070	G=0.996804	C=0.003196
ExAC	Europe	Sub	73234	G=0.99997	C=0.00003
ExAC	Asian	Sub	25134	G=1.00000	C=0.00000
ExAC	American	Sub	11402	G=0.99833	C=0.00167
ExAC	African	Sub	10394	G=0.96488	C=0.03512
ExAC	Other	Sub	906	G=0.999	C=0.001
Allele Frequency Aggregator	Total	Global	110176	G=0.998548	C=0.001452
Allele Frequency Aggregator	European	Sub	92452	G=0.99999	C=0.00001
Allele Frequency Aggregator	Other	Sub	8024	G=0.9984	C=0.0016
Allele Frequency Aggregator	African	Sub	4360	G=0.9683	C=0.0317
Allele Frequency Aggregator	Asian	Sub	3330	G=1.0000	C=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	946	G=0.998	C=0.002
Allele Frequency Aggregator	Latin American 1	Sub	790	G=0.992	C=0.008
Allele Frequency Aggregator	South Asian	Sub	274	G=1.000	C=0.000
The PAGE Study	Global	Study-wide	78694	G=0.98328	C=0.01672
The PAGE Study	AfricanAmerican	Sub	32514	G=0.96528	C=0.03472
The PAGE Study	Mexican	Sub	10808	G=0.99898	C=0.00102
The PAGE Study	Asian	Sub	8316	G=1.0000	C=0.0000
The PAGE Study	PuertoRican	Sub	7918	G=0.9896	C=0.0104
The PAGE Study	NativeHawaiian	Sub	4534	G=0.9993	C=0.0007
The PAGE Study	Cuban	Sub	4228	G=0.9957	C=0.0043
The PAGE Study	Dominican	Sub	3828	G=0.9898	C=0.0102
The PAGE Study	CentralAmerican	Sub	2450	G=0.9939	C=0.0061
The PAGE Study	SouthAmerican	Sub	1982	G=0.9960	C=0.0040
The PAGE Study	NativeAmerican	Sub	1260	G=0.9913	C=0.0087
The PAGE Study	SouthAsian	Sub	856	G=1.000	C=0.000
GO Exome Sequencing Project	Global	Study-wide	13004	G=0.98800	C=0.01200
GO Exome Sequencing Project	European American	Sub	8598	G=0.9999	C=0.0001
GO Exome Sequencing Project	African American	Sub	4406	G=0.9648	C=0.0352
1000Genomes_30x	Global	Study-wide	6404	G=0.9883	C=0.0117
1000Genomes_30x	African	Sub	1786	G=0.9597	C=0.0403
1000Genomes_30x	Europe	Sub	1266	G=1.0000	C=0.0000
1000Genomes_30x	South Asian	Sub	1202	G=1.0000	C=0.0000
1000Genomes_30x	East Asian	Sub	1170	G=1.0000	C=0.0000
1000Genomes_30x	American	Sub	980	G=0.997	C=0.003
1000Genomes	Global	Study-wide	5008	G=0.9888	C=0.0112
1000Genomes	African	Sub	1322	G=0.9592	C=0.0408
1000Genomes	East Asian	Sub	1008	G=1.0000	C=0.0000
1000Genomes	Europe	Sub	1006	G=1.0000	C=0.0000
1000Genomes	South Asian	Sub	978	G=1.000	C=0.000
1000Genomes	American	Sub	694	G=0.997	C=0.003
MxGDAR/Encodat-PGx	Global	Study-wide	3300	G=0.9988	C=0.0012
MxGDAR/Encodat-PGx	MxGDAR	Sub	3300	G=0.9988	C=0.0012
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	G=0.998	C=0.002
PharmGKB Aggregated	Global	Study-wide	350	G=0.977	C=0.023
PharmGKB Aggregated	PA148416573	Sub	350	G=0.977	C=0.023
Qatari	Global	Study-wide	216	G=0.995	C=0.005
SGDP_PRJ	Global	Study-wide	10	G=0.3	C=0.7

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 12	NC_000012.12:g.21205999G>C
GRCh37.p13 chr 12	NC_000012.11:g.21358933G>C
SLCO1B1 RefSeqGene (LRG_1022)	NG_011745.1:g.79806G>C

Gene: SLCO1B1, solute carrier organic anion transporter family member 1B1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLCO1B1 transcript	NM_006446.5:c.1463G>C	G [GGT] > A [GCT]	Coding Sequence Variant
solute carrier organic anion transporter family member 1B1	NP_006437.3:p.Gly488Ala	G (Gly) > A (Ala)	Missense 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: C (allele ID: 331506 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000355032.3	Rotor syndrome	Likely-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	G=	C
GRCh38.p14 chr 12	NC_000012.12:g.21205999=	NC_000012.12:g.21205999G>C
GRCh37.p13 chr 12	NC_000012.11:g.21358933=	NC_000012.11:g.21358933G>C
SLCO1B1 RefSeqGene (LRG_1022)	NG_011745.1:g.79806=	NG_011745.1:g.79806G>C
SLCO1B1 transcript	NM_006446.5:c.1463=	NM_006446.5:c.1463G>C
SLCO1B1 transcript	NM_006446.4:c.1463=	NM_006446.4:c.1463G>C
solute carrier organic anion transporter family member 1B1	NP_006437.3:p.Gly488=	NP_006437.3:p.Gly488Ala

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#.

71 SubSNP, 14 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	PHARMGKB_AB_DME	ss84165373	Dec 15, 2007 (129)
2	AFFY_DM3_1	ss105434061	Feb 05, 2009 (130)
3	SNP500CANCER	ss105439481	Feb 05, 2009 (130)
4	PMT	ss120239949	Dec 01, 2009 (131)
5	ILLUMINA	ss161045363	Dec 01, 2009 (131)
6	1000GENOMES	ss225645029	Jul 14, 2010 (132)
7	NHLBI-ESP	ss342351478	May 09, 2011 (134)
8	ILLUMINA	ss479253947	Sep 08, 2015 (146)
9	1000GENOMES	ss491038295	May 04, 2012 (137)
10	EXOME_CHIP	ss491465350	May 04, 2012 (137)
11	CLINSEQ_SNP	ss491661713	May 04, 2012 (137)
12	ILLUMINA	ss534392741	Sep 08, 2015 (146)
13	ILLUMINA	ss780908769	Sep 08, 2015 (146)
14	ILLUMINA	ss783596241	Sep 08, 2015 (146)
15	1000GENOMES	ss1344206326	Aug 21, 2014 (142)
16	EVA_EXAC	ss1690819936	Apr 01, 2015 (144)
17	EVA_MGP	ss1711323330	Apr 01, 2015 (144)
18	ILLUMINA	ss1752060045	Sep 08, 2015 (146)
19	ILLUMINA	ss1917871599	Feb 12, 2016 (147)
20	WEILL_CORNELL_DGM	ss1932681776	Feb 12, 2016 (147)
21	ILLUMINA	ss1946333556	Feb 12, 2016 (147)
22	ILLUMINA	ss1946333557	Feb 12, 2016 (147)
23	ILLUMINA	ss1959419527	Feb 12, 2016 (147)
24	ILLUMINA	ss1959419528	Feb 12, 2016 (147)
25	ILLUMINA	ss2095032128	Dec 20, 2016 (150)
26	HUMAN_LONGEVITY	ss2188376945	Dec 20, 2016 (150)
27	ILLUMINA	ss2632934687	Nov 08, 2017 (151)
28	ILLUMINA	ss2710756127	Nov 08, 2017 (151)
29	GNOMAD	ss2739676076	Nov 08, 2017 (151)
30	GNOMAD	ss2748826348	Nov 08, 2017 (151)
31	GNOMAD	ss2908176801	Nov 08, 2017 (151)
32	AFFY	ss2984969945	Nov 08, 2017 (151)
33	AFFY	ss2985612473	Nov 08, 2017 (151)
34	ILLUMINA	ss3021413065	Nov 08, 2017 (151)
35	ILLUMINA	ss3021413066	Nov 08, 2017 (151)
36	CSIRBIOHTS	ss3029638279	Nov 08, 2017 (151)
37	ILLUMINA	ss3625617418	Oct 12, 2018 (152)
38	ILLUMINA	ss3626833468	Oct 12, 2018 (152)
39	ILLUMINA	ss3626833469	Oct 12, 2018 (152)
40	ILLUMINA	ss3634494986	Oct 12, 2018 (152)
41	ILLUMINA	ss3636179289	Oct 12, 2018 (152)
42	ILLUMINA	ss3640202319	Oct 12, 2018 (152)
43	ILLUMINA	ss3644586514	Oct 12, 2018 (152)
44	ILLUMINA	ss3644586515	Oct 12, 2018 (152)
45	ILLUMINA	ss3651787218	Oct 12, 2018 (152)
46	ILLUMINA	ss3651787219	Oct 12, 2018 (152)
47	ILLUMINA	ss3651787220	Oct 12, 2018 (152)
48	ILLUMINA	ss3653742493	Oct 12, 2018 (152)
49	ILLUMINA	ss3725309328	Jul 13, 2019 (153)
50	ILLUMINA	ss3744096308	Jul 13, 2019 (153)
51	ILLUMINA	ss3744392921	Jul 13, 2019 (153)
52	ILLUMINA	ss3744795699	Jul 13, 2019 (153)
53	PAGE_CC	ss3771679189	Jul 13, 2019 (153)
54	ILLUMINA	ss3772295222	Jul 13, 2019 (153)
55	KHV_HUMAN_GENOMES	ss3815548565	Jul 13, 2019 (153)
56	EVA	ss3824711279	Apr 26, 2020 (154)
57	SGDP_PRJ	ss3877845102	Apr 26, 2020 (154)
58	EVA	ss3984449733	Apr 26, 2021 (155)
59	EVA	ss3986562229	Apr 26, 2021 (155)
60	TOPMED	ss4911213448	Apr 26, 2021 (155)
61	1000G_HIGH_COVERAGE	ss5290065286	Oct 13, 2022 (156)
62	EVA	ss5404382483	Oct 13, 2022 (156)
63	HUGCELL_USP	ss5484925292	Oct 13, 2022 (156)
64	EVA	ss5512473931	Oct 13, 2022 (156)
65	1000G_HIGH_COVERAGE	ss5587121985	Oct 13, 2022 (156)
66	SANFORD_IMAGENETICS	ss5624296737	Oct 13, 2022 (156)
67	SANFORD_IMAGENETICS	ss5652740205	Oct 13, 2022 (156)
68	EVA	ss5847662884	Oct 13, 2022 (156)
69	EVA	ss5903574649	Oct 13, 2022 (156)
70	EVA	ss5944090790	Oct 13, 2022 (156)
71	EVA	ss5979385044	Oct 13, 2022 (156)
72	1000Genomes	NC_000012.11 - 21358933	Oct 12, 2018 (152)
73	1000Genomes_30x	NC_000012.12 - 21205999	Oct 13, 2022 (156)
74	ExAC	NC_000012.11 - 21358933	Oct 12, 2018 (152)
75	gnomAD - Genomes	NC_000012.12 - 21205999	Apr 26, 2021 (155)
76	gnomAD - Exomes	NC_000012.11 - 21358933	Jul 13, 2019 (153)
77	GO Exome Sequencing Project	NC_000012.11 - 21358933	Oct 12, 2018 (152)
78	Medical Genome Project healthy controls from Spanish population	NC_000012.11 - 21358933	Apr 26, 2020 (154)
79	The PAGE Study	NC_000012.12 - 21205999	Jul 13, 2019 (153)
80	MxGDAR/Encodat-PGx	NC_000012.11 - 21358933	Apr 26, 2021 (155)
81	PharmGKB Aggregated	NC_000012.12 - 21205999	Apr 26, 2020 (154)
82	Qatari	NC_000012.11 - 21358933	Apr 26, 2020 (154)
83	SGDP_PRJ	NC_000012.11 - 21358933	Apr 26, 2020 (154)
84	TopMed	NC_000012.12 - 21205999	Apr 26, 2021 (155)
85	ALFA	NC_000012.12 - 21205999	Apr 26, 2021 (155)
86	ClinVar	RCV000355032.3	Oct 13, 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
ss161045363, ss491661713	NC_000012.10:21250199:G:C	NC_000012.12:21205998:G:C	(self)
56924978, 1109908, 8904054, 1168765, 439090, 2734, 14723706, 29862082, ss225645029, ss342351478, ss479253947, ss491038295, ss491465350, ss534392741, ss780908769, ss783596241, ss1344206326, ss1690819936, ss1711323330, ss1752060045, ss1917871599, ss1932681776, ss1946333556, ss1946333557, ss1959419527, ss1959419528, ss2095032128, ss2632934687, ss2710756127, ss2739676076, ss2748826348, ss2908176801, ss2984969945, ss2985612473, ss3021413065, ss3021413066, ss3029638279, ss3625617418, ss3626833468, ss3626833469, ss3634494986, ss3636179289, ss3640202319, ss3644586514, ss3644586515, ss3651787218, ss3651787219, ss3651787220, ss3653742493, ss3744096308, ss3744392921, ss3744795699, ss3772295222, ss3824711279, ss3877845102, ss3984449733, ss3986562229, ss5404382483, ss5512473931, ss5624296737, ss5652740205, ss5847662884, ss5944090790, ss5979385044	NC_000012.11:21358932:G:C	NC_000012.12:21205998:G:C	(self)
RCV000355032.3, 74647920, 401385108, 900658, 2689, 126759105, 9238602758, ss2188376945, ss3725309328, ss3771679189, ss3815548565, ss4911213448, ss5290065286, ss5484925292, ss5587121985, ss5903574649	NC_000012.12:21205998:G:C	NC_000012.12:21205998:G:C	(self)
ss84165373, ss105434061, ss105439481, ss120239949	NT_009714.17:14119056:G:C	NC_000012.12:21205998:G:C	(self)

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

6 citations for rs59502379

PMID	Title	Author	Year	Journal
24909419	A 30-years review on pharmacokinetics of antibiotics: is the right time for pharmacogenetics?	Baietto L et al.	2014	Current drug metabolism
24944790	Screening for 392 polymorphisms in 141 pharmacogenes.	Kim JY et al.	2014	Biomedical reports
26929901	Frequencies of single-nucleotide polymorphisms and haplotypes of the SLCO1B1 gene in selected populations of the western balkans.	Grapci AD et al.	2015	Balkan journal of medical genetics
29193749	Clinical Implementation of Pharmacogenetic Testing in a Hospital of the Spanish National Health System: Strategy and Experience Over 3 Years.	Borobia AM et al.	2018	Clinical and translational science
33875422	Pharmacogene Sequencing of a Gabonese Population with Severe Plasmodium falciparum Malaria Reveals Multiple Novel Variants with Putative Relevance for Antimalarial Treatment.	Pernaute-Lau L et al.	2021	Antimicrobial agents and chemotherapy
34621706	Comprehensive analysis of important pharmacogenes in Koreans using the DMET™ platform.	Kim B et al.	2021	Translational and clinical pharmacology

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

rs59502379