Name: rs17886522
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.

rs17886522

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:94850018 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.008754 (2317/264690, TOPMED)
C=0.006803 (1709/251204, GnomAD_exome)
C=0.007804 (1094/140190, GnomAD) (+ 17 more)
C=0.007390 (896/121240, ExAC)
C=0.00227 (112/49334, ALFA)
C=0.13214 (3734/28258, 14KJPN)
C=0.13210 (2214/16760, 8.3KJPN)
C=0.00623 (81/13004, GO-ESP)
C=0.0212 (136/6404, 1000G_30x)
C=0.0216 (108/5008, 1000G)
C=0.0007 (3/4480, Estonian)
C=0.0005 (2/3854, ALSPAC)
C=0.0003 (1/3708, TWINSUK)
C=0.0986 (288/2922, KOREAN)
C=0.0928 (170/1832, Korea1K)
C=0.002 (1/534, MGP)
C=0.051 (18/356, PharmGKB)
C=0.019 (4/216, Qatari)
C=0.019 (4/212, Vietnamese)
A=0.48 (20/42, SGDP_PRJ)

Clinical Significance: Reported in ClinVar
Gene : Consequence: CYP2C19 : Synonymous Variant
Publications: 5 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	65650	A=0.99653	C=0.00347
European	Sub	47358	A=0.99979	C=0.00021
African	Sub	8398	A=0.9799	C=0.0201
African Others	Sub	306	A=0.987	C=0.013
African American	Sub	8092	A=0.9796	C=0.0204
Asian	Sub	168	A=0.869	C=0.131
East Asian	Sub	112	A=0.884	C=0.116
Other Asian	Sub	56	A=0.84	C=0.16
Latin American 1	Sub	500	A=0.992	C=0.008
Latin American 2	Sub	628	A=0.998	C=0.002
South Asian	Sub	98	A=0.99	C=0.01
Other	Sub	8500	A=0.9975	C=0.0025

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=0.991246	C=0.008754
gnomAD - Exomes	Global	Study-wide	251204	A=0.993197	C=0.006803
gnomAD - Exomes	European	Sub	135250	A=0.999741	C=0.000259
gnomAD - Exomes	Asian	Sub	48994	A=0.97355	C=0.02645
gnomAD - Exomes	American	Sub	34506	A=0.99925	C=0.00075
gnomAD - Exomes	African	Sub	16248	A=0.97944	C=0.02056
gnomAD - Exomes	Ashkenazi Jewish	Sub	10078	A=1.00000	C=0.00000
gnomAD - Exomes	Other	Sub	6128	A=0.9971	C=0.0029
gnomAD - Genomes	Global	Study-wide	140190	A=0.992196	C=0.007804
gnomAD - Genomes	European	Sub	75946	A=0.99979	C=0.00021
gnomAD - Genomes	African	Sub	42008	A=0.97941	C=0.02059
gnomAD - Genomes	American	Sub	13628	A=0.99846	C=0.00154
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=1.0000	C=0.0000
gnomAD - Genomes	East Asian	Sub	3132	A=0.9457	C=0.0543
gnomAD - Genomes	Other	Sub	2152	A=0.9898	C=0.0102
ExAC	Global	Study-wide	121240	A=0.992610	C=0.007390
ExAC	Europe	Sub	73320	A=0.99977	C=0.00023
ExAC	Asian	Sub	25152	A=0.97444	C=0.02556
ExAC	American	Sub	11470	A=0.99904	C=0.00096
ExAC	African	Sub	10390	A=0.97844	C=0.02156
ExAC	Other	Sub	908	A=0.999	C=0.001
Allele Frequency Aggregator	Total	Global	49334	A=0.99773	C=0.00227
Allele Frequency Aggregator	European	Sub	37296	A=0.99973	C=0.00027
Allele Frequency Aggregator	Other	Sub	7070	A=0.9976	C=0.0024
Allele Frequency Aggregator	African	Sub	3574	A=0.9841	C=0.0159
Allele Frequency Aggregator	Latin American 2	Sub	628	A=0.998	C=0.002
Allele Frequency Aggregator	Latin American 1	Sub	500	A=0.992	C=0.008
Allele Frequency Aggregator	Asian	Sub	168	A=0.869	C=0.131
Allele Frequency Aggregator	South Asian	Sub	98	A=0.99	C=0.01
14KJPN	JAPANESE	Study-wide	28258	A=0.86786	C=0.13214
8.3KJPN	JAPANESE	Study-wide	16760	A=0.86790	C=0.13210
GO Exome Sequencing Project	Global	Study-wide	13004	A=0.99377	C=0.00623
GO Exome Sequencing Project	European American	Sub	8598	A=0.9997	C=0.0003
GO Exome Sequencing Project	African American	Sub	4406	A=0.9823	C=0.0177
1000Genomes_30x	Global	Study-wide	6404	A=0.9788	C=0.0212
1000Genomes_30x	African	Sub	1786	A=0.9698	C=0.0302
1000Genomes_30x	Europe	Sub	1266	A=1.0000	C=0.0000
1000Genomes_30x	South Asian	Sub	1202	A=0.9859	C=0.0141
1000Genomes_30x	East Asian	Sub	1170	A=0.9462	C=0.0538
1000Genomes_30x	American	Sub	980	A=0.998	C=0.002
1000Genomes	Global	Study-wide	5008	A=0.9784	C=0.0216
1000Genomes	African	Sub	1322	A=0.9705	C=0.0295
1000Genomes	East Asian	Sub	1008	A=0.9444	C=0.0556
1000Genomes	Europe	Sub	1006	A=1.0000	C=0.0000
1000Genomes	South Asian	Sub	978	A=0.988	C=0.012
1000Genomes	American	Sub	694	A=0.999	C=0.001
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9993	C=0.0007
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9995	C=0.0005
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9997	C=0.0003
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.9014	C=0.0986
Korean Genome Project	KOREAN	Study-wide	1832	A=0.9072	C=0.0928
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	A=0.998	C=0.002
PharmGKB Aggregated	Global	Study-wide	356	A=0.949	C=0.051
PharmGKB Aggregated	PA150061598	Sub	356	A=0.949	C=0.051
Qatari	Global	Study-wide	216	A=0.981	C=0.019
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.981	C=0.019
SGDP_PRJ	Global	Study-wide	42	A=0.48	C=0.52

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 10	NC_000010.11:g.94850018A>C
GRCh37.p13 chr 10	NC_000010.10:g.96609775A>C
CYP2C19 RefSeqGene (LRG_584)	NG_008384.3:g.92338A>C

Gene: CYP2C19, cytochrome P450 family 2 subfamily C member 19 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CYP2C19 transcript	NM_000769.4:c.1251A>C	G [GGA] > G [GGC]	Coding Sequence Variant
cytochrome P450 2C19	NP_000760.1:p.Gly417=	G (Gly) > G (Gly)	Synonymous 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: 1267768 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001687793.1	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	A=	C
GRCh38.p14 chr 10	NC_000010.11:g.94850018=	NC_000010.11:g.94850018A>C
GRCh37.p13 chr 10	NC_000010.10:g.96609775=	NC_000010.10:g.96609775A>C
CYP2C19 RefSeqGene (LRG_584)	NG_008384.3:g.92338=	NG_008384.3:g.92338A>C
CYP2C19 transcript	NM_000769.4:c.1251=	NM_000769.4:c.1251A>C
CYP2C19 transcript	NM_000769.3:c.1251=	NM_000769.3:c.1251A>C
CYP2C19 transcript	NM_000769.2:c.1251=	NM_000769.2:c.1251A>C
CYP2C19 transcript	NM_000769.1:c.1251=	NM_000769.1:c.1251A>C
cytochrome P450 2C19	NP_000760.1:p.Gly417=	NP_000760.1:p.Gly417=

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#.

50 SubSNP, 20 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	EGP_SNPS	ss28531464	Dec 02, 2004 (124)
2	BIOVENTURES	ss32475268	May 24, 2005 (125)
3	CGM_KYOTO	ss76860186	Dec 06, 2007 (129)
4	CCHMC-CAE-PGCORE	ss79314161	Dec 15, 2007 (130)
5	PHARMGKB_AB_DME	ss84155599	Dec 15, 2007 (130)
6	SNP500CANCER	ss105439385	Feb 05, 2009 (130)
7	GMI	ss280732581	May 04, 2012 (137)
8	1000GENOMES	ss336318023	May 09, 2011 (134)
9	NHLBI-ESP	ss342304139	May 09, 2011 (134)
10	1000GENOMES	ss491001653	May 04, 2012 (137)
11	CLINSEQ_SNP	ss491629952	May 04, 2012 (137)
12	TISHKOFF	ss562143165	Apr 25, 2013 (138)
13	SSMP	ss657184836	Apr 25, 2013 (138)
14	JMKIDD_LAB	ss1067514955	Aug 21, 2014 (142)
15	JMKIDD_LAB	ss1077215921	Aug 21, 2014 (142)
16	1000GENOMES	ss1338626536	Aug 21, 2014 (142)
17	EVA_UK10K_ALSPAC	ss1625197287	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1668191320	Apr 01, 2015 (144)
19	EVA_EXAC	ss1690012193	Apr 01, 2015 (144)
20	EVA_MGP	ss1711265791	Apr 01, 2015 (144)
21	WEILL_CORNELL_DGM	ss1931171361	Feb 12, 2016 (147)
22	HUMAN_LONGEVITY	ss2177153771	Dec 20, 2016 (150)
23	SYSTEMSBIOZJU	ss2627625893	Nov 08, 2017 (151)
24	GRF	ss2698843426	Nov 08, 2017 (151)
25	GNOMAD	ss2738421162	Nov 08, 2017 (151)
26	GNOMAD	ss2748441595	Nov 08, 2017 (151)
27	GNOMAD	ss2892136520	Nov 08, 2017 (151)
28	SWEGEN	ss3006967294	Nov 08, 2017 (151)
29	CSIRBIOHTS	ss3029638031	Nov 08, 2017 (151)
30	EGCUT_WGS	ss3674379295	Jul 13, 2019 (153)
31	EVA	ss3748469067	Jul 13, 2019 (153)
32	KHV_HUMAN_GENOMES	ss3813835545	Jul 13, 2019 (153)
33	EVA	ss3824541000	Apr 26, 2020 (154)
34	SGDP_PRJ	ss3874829166	Apr 26, 2020 (154)
35	KRGDB	ss3922957465	Apr 26, 2020 (154)
36	KOGIC	ss3968459691	Apr 26, 2020 (154)
37	EVA	ss3986493477	Apr 26, 2021 (155)
38	TOPMED	ss4862652360	Apr 26, 2021 (155)
39	TOMMO_GENOMICS	ss5198972260	Apr 26, 2021 (155)
40	EVA	ss5236886083	Apr 26, 2021 (155)
41	1000G_HIGH_COVERAGE	ss5285090604	Oct 16, 2022 (156)
42	EVA	ss5395327254	Oct 16, 2022 (156)
43	HUGCELL_USP	ss5480549737	Oct 16, 2022 (156)
44	EVA	ss5512473902	Oct 16, 2022 (156)
45	1000G_HIGH_COVERAGE	ss5579568958	Oct 16, 2022 (156)
46	SANFORD_IMAGENETICS	ss5649887533	Oct 16, 2022 (156)
47	TOMMO_GENOMICS	ss5745191208	Oct 16, 2022 (156)
48	YY_MCH	ss5811792976	Oct 16, 2022 (156)
49	EVA	ss5880088383	Oct 16, 2022 (156)
50	EVA	ss5941173825	Oct 16, 2022 (156)
51	1000Genomes	NC_000010.10 - 96609775	Oct 12, 2018 (152)
52	1000Genomes_30x	NC_000010.11 - 94850018	Oct 16, 2022 (156)
53	The Avon Longitudinal Study of Parents and Children	NC_000010.10 - 96609775	Oct 12, 2018 (152)
54	Genetic variation in the Estonian population	NC_000010.10 - 96609775	Oct 12, 2018 (152)
55	ExAC	NC_000010.10 - 96609775	Oct 12, 2018 (152)
56	gnomAD - Genomes	NC_000010.11 - 94850018	Apr 26, 2021 (155)
57	gnomAD - Exomes	NC_000010.10 - 96609775	Jul 13, 2019 (153)
58	GO Exome Sequencing Project	NC_000010.10 - 96609775	Oct 12, 2018 (152)
59	KOREAN population from KRGDB	NC_000010.10 - 96609775	Apr 26, 2020 (154)
60	Korean Genome Project	NC_000010.11 - 94850018	Apr 26, 2020 (154)
61	Medical Genome Project healthy controls from Spanish population	NC_000010.10 - 96609775	Apr 26, 2020 (154)
62	PharmGKB Aggregated	NC_000010.11 - 94850018	Apr 26, 2020 (154)
63	Qatari	NC_000010.10 - 96609775	Apr 26, 2020 (154)
64	SGDP_PRJ	NC_000010.10 - 96609775	Apr 26, 2020 (154)
65	8.3KJPN	NC_000010.10 - 96609775	Apr 26, 2021 (155)
66	14KJPN	NC_000010.11 - 94850018	Oct 16, 2022 (156)
67	TopMed	NC_000010.11 - 94850018	Apr 26, 2021 (155)
68	UK 10K study - Twins	NC_000010.10 - 96609775	Oct 12, 2018 (152)
69	A Vietnamese Genetic Variation Database	NC_000010.10 - 96609775	Jul 13, 2019 (153)
70	ALFA	NC_000010.11 - 94850018	Apr 26, 2021 (155)
71	ClinVar	RCV001687793.1	Oct 16, 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).

Associated ID	History Updated (Build)
rs59521943	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss280732581, ss491629952	NC_000010.9:96599764:A:C	NC_000010.11:94850017:A:C	(self)
51058038, 28346921, 20117543, 241841, 7620986, 998682, 30134859, 381551, 13213291, 26846146, 56941567, 28346921, 6294668, ss336318023, ss342304139, ss491001653, ss562143165, ss657184836, ss1067514955, ss1077215921, ss1338626536, ss1625197287, ss1668191320, ss1690012193, ss1711265791, ss1931171361, ss2627625893, ss2698843426, ss2738421162, ss2748441595, ss2892136520, ss3006967294, ss3029638031, ss3674379295, ss3748469067, ss3824541000, ss3874829166, ss3922957465, ss3986493477, ss5198972260, ss5395327254, ss5512473902, ss5649887533, ss5941173825	NC_000010.10:96609774:A:C	NC_000010.11:94850017:A:C	(self)
RCV001687793.1, 67094893, 360757811, 24837692, 1142, 79028312, 78198015, 13903263552, ss2177153771, ss3813835545, ss3968459691, ss4862652360, ss5236886083, ss5285090604, ss5480549737, ss5579568958, ss5745191208, ss5811792976, ss5880088383	NC_000010.11:94850017:A:C	NC_000010.11:94850017:A:C	(self)
ss28531464, ss32475268, ss76860186, ss79314161, ss84155599, ss105439385	NT_030059.13:47414238:A:C	NC_000010.11:94850017:A:C	(self)

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

5 citations for rs17886522

PMID	Title	Author	Year	Journal
19164093	Novel variants of major drug-metabolising enzyme genes in diverse African populations and their predicted functional effects.	Matimba A et al.	2009	Human genomics
24944790	Screening for 392 polymorphisms in 141 pharmacogenes.	Kim JY et al.	2014	Biomedical reports
26781306	Genotype‑phenotype analysis of CYP2C19 in the Tibetan population and its potential clinical implications in drug therapy.	Jin T et al.	2016	Molecular medicine reports
26785747	Polymorphisms in genes involved in the absorption, distribution, metabolism, and excretion of drugs in the Kazakhs of Kazakhstan.	Iskakova AN et al.	2016	BMC genetics
29681089	Genetic variation in biotransformation enzymes, air pollution exposures, and risk of spina bifida.	Padula AM et al.	2018	American journal of medical genetics. Part A

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

rs17886522