Name: rs79042365
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.

rs79042365

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:20855051 (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=0.006117 (1619/264690, TOPMED)
G=0.001493 (373/249912, GnomAD_exome)
G=0.006065 (850/140150, GnomAD) (+ 13 more)
G=0.001832 (218/118976, ExAC)
G=0.000899 (99/110116, ALFA)
G=0.00905 (712/78700, PAGE_STUDY)
G=0.00723 (94/13004, GO-ESP)
G=0.0070 (45/6404, 1000G_30x)
G=0.0056 (28/5008, 1000G)
G=0.0003 (1/3854, ALSPAC)
G=0.0000 (0/3708, TWINSUK)
G=0.0030 (10/3284, PRJNA289433)
G=0.006 (3/536, PharmGKB)
G=0.005 (1/216, Qatari)
C=0.5 (1/2, SGDP_PRJ)
G=0.5 (1/2, SGDP_PRJ)

Clinical Significance: Reported in ClinVar
Gene : Consequence: SLCO1B3 : Missense Variant
SLCO1B3-SLCO1B7 : Missense 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	110116	C=0.999101	G=0.000899
European	Sub	92382	C=0.99995	G=0.00005
African	Sub	4360	C=0.9817	G=0.0183
African Others	Sub	174	C=0.977	G=0.023
African American	Sub	4186	C=0.9818	G=0.0182
Asian	Sub	3328	C=1.0000	G=0.0000
East Asian	Sub	2672	C=1.0000	G=0.0000
Other Asian	Sub	656	C=1.000	G=0.000
Latin American 1	Sub	790	C=0.996	G=0.004
Latin American 2	Sub	946	C=0.999	G=0.001
South Asian	Sub	274	C=1.000	G=0.000
Other	Sub	8036	C=0.9988	G=0.0012

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=0.993883	G=0.006117
gnomAD - Exomes	Global	Study-wide	249912	C=0.998507	G=0.001493
gnomAD - Exomes	European	Sub	134860	C=0.999926	G=0.000074
gnomAD - Exomes	Asian	Sub	48614	C=1.00000	G=0.00000
gnomAD - Exomes	American	Sub	34104	C=0.99906	G=0.00094
gnomAD - Exomes	African	Sub	16180	C=0.97973	G=0.02027
gnomAD - Exomes	Ashkenazi Jewish	Sub	10052	C=1.00000	G=0.00000
gnomAD - Exomes	Other	Sub	6102	C=0.9995	G=0.0005
gnomAD - Genomes	Global	Study-wide	140150	C=0.993935	G=0.006065
gnomAD - Genomes	European	Sub	75906	C=0.99997	G=0.00003
gnomAD - Genomes	African	Sub	42002	C=0.98017	G=0.01983
gnomAD - Genomes	American	Sub	13640	C=0.99934	G=0.00066
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=1.0000	G=0.0000
gnomAD - Genomes	East Asian	Sub	3128	C=1.0000	G=0.0000
gnomAD - Genomes	Other	Sub	2154	C=0.9972	G=0.0028
ExAC	Global	Study-wide	118976	C=0.998168	G=0.001832
ExAC	Europe	Sub	71828	C=1.00000	G=0.00000
ExAC	Asian	Sub	24814	C=1.00000	G=0.00000
ExAC	American	Sub	11296	C=0.99903	G=0.00097
ExAC	African	Sub	10142	C=0.97969	G=0.02031
ExAC	Other	Sub	896	C=0.999	G=0.001
Allele Frequency Aggregator	Total	Global	110116	C=0.999101	G=0.000899
Allele Frequency Aggregator	European	Sub	92382	C=0.99995	G=0.00005
Allele Frequency Aggregator	Other	Sub	8036	C=0.9988	G=0.0012
Allele Frequency Aggregator	African	Sub	4360	C=0.9817	G=0.0183
Allele Frequency Aggregator	Asian	Sub	3328	C=1.0000	G=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	946	C=0.999	G=0.001
Allele Frequency Aggregator	Latin American 1	Sub	790	C=0.996	G=0.004
Allele Frequency Aggregator	South Asian	Sub	274	C=1.000	G=0.000
The PAGE Study	Global	Study-wide	78700	C=0.99095	G=0.00905
The PAGE Study	AfricanAmerican	Sub	32516	C=0.98090	G=0.01910
The PAGE Study	Mexican	Sub	10810	C=0.99861	G=0.00139
The PAGE Study	Asian	Sub	8318	C=1.0000	G=0.0000
The PAGE Study	PuertoRican	Sub	7916	C=0.9965	G=0.0035
The PAGE Study	NativeHawaiian	Sub	4534	C=0.9998	G=0.0002
The PAGE Study	Cuban	Sub	4230	C=0.9969	G=0.0031
The PAGE Study	Dominican	Sub	3828	C=0.9945	G=0.0055
The PAGE Study	CentralAmerican	Sub	2450	C=0.9992	G=0.0008
The PAGE Study	SouthAmerican	Sub	1982	C=0.9975	G=0.0025
The PAGE Study	NativeAmerican	Sub	1260	C=0.9952	G=0.0048
The PAGE Study	SouthAsian	Sub	856	C=1.000	G=0.000
GO Exome Sequencing Project	Global	Study-wide	13004	C=0.99277	G=0.00723
GO Exome Sequencing Project	European American	Sub	8600	C=1.0000	G=0.0000
GO Exome Sequencing Project	African American	Sub	4404	C=0.9787	G=0.0213
1000Genomes_30x	Global	Study-wide	6404	C=0.9930	G=0.0070
1000Genomes_30x	African	Sub	1786	C=0.9759	G=0.0241
1000Genomes_30x	Europe	Sub	1266	C=1.0000	G=0.0000
1000Genomes_30x	South Asian	Sub	1202	C=1.0000	G=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	G=0.0000
1000Genomes_30x	American	Sub	980	C=0.998	G=0.002
1000Genomes	Global	Study-wide	5008	C=0.9944	G=0.0056
1000Genomes	African	Sub	1322	C=0.9803	G=0.0197
1000Genomes	East Asian	Sub	1008	C=1.0000	G=0.0000
1000Genomes	Europe	Sub	1006	C=1.0000	G=0.0000
1000Genomes	South Asian	Sub	978	C=1.000	G=0.000
1000Genomes	American	Sub	694	C=0.997	G=0.003
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9997	G=0.0003
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=1.0000	G=0.0000
MxGDAR/Encodat-PGx	Global	Study-wide	3284	C=0.9970	G=0.0030
MxGDAR/Encodat-PGx	MxGDAR	Sub	3284	C=0.9970	G=0.0030
PharmGKB Aggregated	Global	Study-wide	536	C=0.994	G=0.006
PharmGKB Aggregated	PA162976214	Sub	536	C=0.994	G=0.006
Qatari	Global	Study-wide	216	C=0.995	G=0.005
SGDP_PRJ	Global	Study-wide	2	C=0.5	G=0.5

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.20855051C>G
GRCh37.p13 chr 12	NC_000012.11:g.21007985C>G
SLCO1B3 RefSeqGene	NG_032071.1:g.49348C>G

Gene: SLCO1B3, solute carrier organic anion transporter family member 1B3 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLCO1B3 transcript variant 2	NM_001349920.2:c.24C>G	F [TTC] > L [TTG]	Coding Sequence Variant
solute carrier organic anion transporter family member 1B3 isoform 2	NP_001336849.1:p.Phe8Leu	F (Phe) > L (Leu)	Missense Variant
SLCO1B3 transcript variant 1	NM_019844.4:c.108C>G	F [TTC] > L [TTG]	Coding Sequence Variant
solute carrier organic anion transporter family member 1B3 isoform 1	NP_062818.1:p.Phe36Leu	F (Phe) > L (Leu)	Missense Variant

Gene: SLCO1B3-SLCO1B7, SLCO1B3-SLCO1B7 readthrough (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLCO1B3-SLCO1B7 transcript	NM_001371097.1:c.108C>G	F [TTC] > L [TTG]	Coding Sequence Variant
SLCO1B3-SLCO1B7 readthrough transcript protein	NP_001358026.1:p.Phe36Leu	F (Phe) > L (Leu)	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: G (allele ID: 324045 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000318161.3	Rotor syndrome	Benign
RCV000906015.4	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 12	NC_000012.12:g.20855051=	NC_000012.12:g.20855051C>G
GRCh37.p13 chr 12	NC_000012.11:g.21007985=	NC_000012.11:g.21007985C>G
SLCO1B3 RefSeqGene	NG_032071.1:g.49348=	NG_032071.1:g.49348C>G
SLCO1B3 transcript variant 1	NM_019844.4:c.108=	NM_019844.4:c.108C>G
SLCO1B3 transcript variant 1	NM_019844.3:c.108=	NM_019844.3:c.108C>G
SLCO1B3 transcript variant 2	NM_001349920.2:c.24=	NM_001349920.2:c.24C>G
SLCO1B3 transcript variant 2	NM_001349920.1:c.24=	NM_001349920.1:c.24C>G
SLCO1B3-SLCO1B7 transcript	NM_001371097.1:c.108=	NM_001371097.1:c.108C>G
solute carrier organic anion transporter family member 1B3 isoform 1	NP_062818.1:p.Phe36=	NP_062818.1:p.Phe36Leu
solute carrier organic anion transporter family member 1B3 isoform 2	NP_001336849.1:p.Phe8=	NP_001336849.1:p.Phe8Leu
SLCO1B3-SLCO1B7 readthrough transcript protein	NP_001358026.1:p.Phe36=	NP_001358026.1:p.Phe36Leu

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, 15 Frequency, 2 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	SEATTLESEQ	ss159725845	Dec 01, 2009 (131)
2	ILLUMINA	ss161045350	Dec 01, 2009 (131)
3	1000GENOMES	ss225643560	Jul 14, 2010 (132)
4	PHARMGKB_PMT	ss290492812	May 09, 2011 (134)
5	NHLBI-ESP	ss342351373	May 09, 2011 (134)
6	ILLUMINA	ss479331206	Sep 08, 2015 (146)
7	1000GENOMES	ss491038172	May 04, 2012 (137)
8	EXOME_CHIP	ss491465259	May 04, 2012 (137)
9	ILLUMINA	ss535114476	Sep 08, 2015 (146)
10	TISHKOFF	ss563037753	Apr 25, 2013 (138)
11	ILLUMINA	ss780908705	Aug 21, 2014 (142)
12	ILLUMINA	ss783596176	Aug 21, 2014 (142)
13	JMKIDD_LAB	ss974482862	Aug 21, 2014 (142)
14	PMT	ss1040223708	Apr 01, 2015 (144)
15	1000GENOMES	ss1344195174	Aug 21, 2014 (142)
16	EVA_UK10K_ALSPAC	ss1628161615	Apr 01, 2015 (144)
17	EVA_UK10K_TWINSUK	ss1671155648	Apr 01, 2015 (144)
18	EVA_EXAC	ss1690818182	Apr 01, 2015 (144)
19	ILLUMINA	ss1752059740	Sep 08, 2015 (146)
20	ILLUMINA	ss1917871531	Feb 12, 2016 (147)
21	WEILL_CORNELL_DGM	ss1932678711	Feb 12, 2016 (147)
22	ILLUMINA	ss1946333424	Feb 12, 2016 (147)
23	ILLUMINA	ss1959419233	Feb 12, 2016 (147)
24	HUMAN_LONGEVITY	ss2188354464	Dec 20, 2016 (150)
25	ILLUMINA	ss2632934293	Nov 08, 2017 (151)
26	ILLUMINA	ss2710755979	Nov 08, 2017 (151)
27	GNOMAD	ss2739673456	Nov 08, 2017 (151)
28	GNOMAD	ss2748825528	Nov 08, 2017 (151)
29	GNOMAD	ss2908145906	Nov 08, 2017 (151)
30	AFFY	ss2984969838	Nov 08, 2017 (151)
31	ILLUMINA	ss3021412760	Nov 08, 2017 (151)
32	ILLUMINA	ss3626832795	Oct 12, 2018 (152)
33	ILLUMINA	ss3626832796	Oct 12, 2018 (152)
34	ILLUMINA	ss3634494691	Oct 12, 2018 (152)
35	ILLUMINA	ss3636179000	Oct 12, 2018 (152)
36	ILLUMINA	ss3640202024	Oct 12, 2018 (152)
37	ILLUMINA	ss3644586385	Oct 12, 2018 (152)
38	ILLUMINA	ss3651786830	Oct 12, 2018 (152)
39	ILLUMINA	ss3653742359	Oct 12, 2018 (152)
40	ILLUMINA	ss3725309049	Jul 13, 2019 (153)
41	ILLUMINA	ss3744392849	Jul 13, 2019 (153)
42	ILLUMINA	ss3744795404	Jul 13, 2019 (153)
43	PAGE_CC	ss3771678978	Jul 13, 2019 (153)
44	ILLUMINA	ss3772294929	Jul 13, 2019 (153)
45	EVA	ss3824710830	Apr 26, 2020 (154)
46	SGDP_PRJ	ss3877839278	Apr 26, 2020 (154)
47	EVA	ss3984449694	Apr 26, 2021 (155)
48	TOPMED	ss4911119411	Apr 26, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5290055564	Oct 13, 2022 (156)
50	EVA	ss5404367881	Oct 13, 2022 (156)
51	HUGCELL_USP	ss5484916913	Oct 13, 2022 (156)
52	1000G_HIGH_COVERAGE	ss5587107063	Oct 13, 2022 (156)
53	SANFORD_IMAGENETICS	ss5652734160	Oct 13, 2022 (156)
54	EVA	ss5847662749	Oct 13, 2022 (156)
55	EVA	ss5903563538	Oct 13, 2022 (156)
56	EVA	ss5944084790	Oct 13, 2022 (156)
57	1000Genomes	NC_000012.11 - 21007985	Oct 12, 2018 (152)
58	1000Genomes_30x	NC_000012.12 - 20855051	Oct 13, 2022 (156)
59	The Avon Longitudinal Study of Parents and Children	NC_000012.11 - 21007985	Oct 12, 2018 (152)
60	ExAC	NC_000012.11 - 21007985	Oct 12, 2018 (152)
61	gnomAD - Genomes	NC_000012.12 - 20855051	Apr 26, 2021 (155)
62	gnomAD - Exomes	NC_000012.11 - 21007985	Jul 13, 2019 (153)
63	GO Exome Sequencing Project	NC_000012.11 - 21007985	Oct 12, 2018 (152)
64	The PAGE Study	NC_000012.12 - 20855051	Jul 13, 2019 (153)
65	MxGDAR/Encodat-PGx	NC_000012.11 - 21007985	Apr 26, 2021 (155)
66	PharmGKB Aggregated	NC_000012.12 - 20855051	Apr 26, 2020 (154)
67	Qatari	NC_000012.11 - 21007985	Apr 26, 2020 (154)
68	SGDP_PRJ	NC_000012.11 - 21007985	Apr 26, 2020 (154)
69	TopMed	NC_000012.12 - 20855051	Apr 26, 2021 (155)
70	UK 10K study - Twins	NC_000012.11 - 21007985	Oct 12, 2018 (152)
71	ALFA	NC_000012.12 - 20855051	Apr 26, 2021 (155)
72	ClinVar	RCV000318161.3	Oct 13, 2022 (156)
73	ClinVar	RCV000906015.4	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
ss161045350	NC_000012.10:20899251:C:G	NC_000012.12:20855050:C:G	(self)
56913451, 31601633, 1107955, 8901365, 1168315, 2695, 14720641, 29856258, 31601633, ss225643560, ss342351373, ss479331206, ss491038172, ss491465259, ss535114476, ss563037753, ss780908705, ss783596176, ss974482862, ss1344195174, ss1628161615, ss1671155648, ss1690818182, ss1752059740, ss1917871531, ss1932678711, ss1946333424, ss1959419233, ss2632934293, ss2710755979, ss2739673456, ss2748825528, ss2908145906, ss2984969838, ss3021412760, ss3626832795, ss3626832796, ss3634494691, ss3636179000, ss3640202024, ss3644586385, ss3651786830, ss3653742359, ss3744392849, ss3744795404, ss3772294929, ss3824710830, ss3877839278, ss3984449694, ss5404367881, ss5652734160, ss5847662749, ss5944084790	NC_000012.11:21007984:C:G	NC_000012.12:20855050:C:G	(self)
RCV000318161.3, RCV000906015.4, 74632998, 401307590, 900447, 2581, 126665068, 1825341855, ss2188354464, ss3725309049, ss3771678978, ss4911119411, ss5290055564, ss5484916913, ss5587107063, ss5903563538	NC_000012.12:20855050:C:G	NC_000012.12:20855050:C:G	(self)
ss159725845, ss290492812	NT_009714.17:13768108:C:G	NC_000012.12:20855050:C:G	(self)
ss1040223708	NT_009714.18:13770400:C:G	NC_000012.12:20855050:C: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 rs79042365

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

rs79042365