Name: rs1058164
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.

rs1058164

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:42129130 (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 / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.425384 (112595/264690, TOPMED)
C=0.427506 (59266/138632, GnomAD)
C=0.46516 (13098/28158, 14KJPN) (+ 2 more)
C=0.42393 (11687/27568, ALFA)
C=0.4049 (2593/6404, 1000G_30x)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CYP2D6 : Synonymous Variant
LOC102723722 : 2KB Upstream Variant
Publications: 15 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	27568	C=0.42393	G=0.57607	0.196024	0.348157	0.455818	32
European	Sub	20254	C=0.43216	G=0.56784	0.199171	0.334847	0.465982	14
African	Sub	3504	C=0.3656	G=0.6344	0.156393	0.425228	0.418379	10
African Others	Sub	122	C=0.402	G=0.598	0.163934	0.360656	0.47541	0
African American	Sub	3382	C=0.3643	G=0.6357	0.156121	0.427558	0.416322	10
Asian	Sub	168	C=0.274	G=0.726	0.095238	0.547619	0.357143	1
East Asian	Sub	112	C=0.277	G=0.723	0.142857	0.589286	0.267857	4
Other Asian	Sub	56	C=0.27	G=0.73	0.0	0.464286	0.535714	2
Latin American 1	Sub	146	C=0.432	G=0.568	0.219178	0.356164	0.424658	1
Latin American 2	Sub	610	C=0.579	G=0.421	0.347541	0.190164	0.462295	1
South Asian	Sub	98	C=0.39	G=0.61	0.22449	0.44898	0.326531	3
Other	Sub	2788	C=0.4136	G=0.5864	0.193687	0.366571	0.439742	7

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=0.425384	G=0.574616
gnomAD - Genomes	Global	Study-wide	138632	C=0.427506	G=0.572494
gnomAD - Genomes	European	Sub	75214	C=0.45545	G=0.54455
gnomAD - Genomes	African	Sub	41312	C=0.36387	G=0.63613
gnomAD - Genomes	American	Sub	13554	C=0.51335	G=0.48665
gnomAD - Genomes	Ashkenazi Jewish	Sub	3308	C=0.3625	G=0.6375
gnomAD - Genomes	East Asian	Sub	3110	C=0.2913	G=0.7087
gnomAD - Genomes	Other	Sub	2134	C=0.4288	G=0.5712
14KJPN	JAPANESE	Study-wide	28158	C=0.46516	G=0.53484
Allele Frequency Aggregator	Total	Global	27568	C=0.42393	G=0.57607
Allele Frequency Aggregator	European	Sub	20254	C=0.43216	G=0.56784
Allele Frequency Aggregator	African	Sub	3504	C=0.3656	G=0.6344
Allele Frequency Aggregator	Other	Sub	2788	C=0.4136	G=0.5864
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.579	G=0.421
Allele Frequency Aggregator	Asian	Sub	168	C=0.274	G=0.726
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.432	G=0.568
Allele Frequency Aggregator	South Asian	Sub	98	C=0.39	G=0.61
1000Genomes_30x	Global	Study-wide	6404	C=0.4049	G=0.5951
1000Genomes_30x	African	Sub	1786	C=0.3270	G=0.6730
1000Genomes_30x	Europe	Sub	1266	C=0.4613	G=0.5387
1000Genomes_30x	South Asian	Sub	1202	C=0.4709	G=0.5291
1000Genomes_30x	East Asian	Sub	1170	C=0.2889	G=0.7111
1000Genomes_30x	American	Sub	980	C=0.532	G=0.468

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.42129130C>G
GRCh38.p14 chr 22	NC_000022.11:g.42129130C>T
gene/pseudogene RefSeqGene (LRG_303)	NG_008376.4:g.6681G>C
gene/pseudogene RefSeqGene (LRG_303)	NG_008376.4:g.6681G>A
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1	NW_015148968.1:g.6871G>C
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1	NW_015148968.1:g.6871G>T
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1	NW_014040931.1:g.22719G>C
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1	NW_014040931.1:g.22719G>T
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1	NW_009646208.1:g.14696G>C
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1	NW_009646208.1:g.14696G>T
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1	NW_004504305.1:g.51457G>C
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1	NW_004504305.1:g.51457G>T
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1	NT_187682.1:g.51471G>C
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1	NT_187682.1:g.51471G>T
GRCh37.p13 chr 22	NC_000022.10:g.42525132G>C
GRCh37.p13 chr 22	NC_000022.10:g.42525132G>T

Gene: CYP2D6, cytochrome P450 family 2 subfamily D member 6 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CYP2D6 transcript variant 2	NM_001025161.3:c.353-186G… NM_001025161.3:c.353-186G>C	N/A	Intron Variant
CYP2D6 transcript variant 1	NM_000106.6:c.408G>C	V [GTG] > V [GTC]	Coding Sequence Variant
cytochrome P450 2D6 isoform 1	NP_000097.3:p.Val136=	V (Val) > V (Val)	Synonymous Variant
CYP2D6 transcript variant 1	NM_000106.6:c.408G>A	V [GTG] > V [GTA]	Coding Sequence Variant
cytochrome P450 2D6 isoform 1	NP_000097.3:p.Val136=	V (Val) > V (Val)	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.

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	C=	G	T
GRCh38.p14 chr 22	NC_000022.11:g.42129130=	NC_000022.11:g.42129130C>G	NC_000022.11:g.42129130C>T
gene/pseudogene RefSeqGene (LRG_303)	NG_008376.4:g.6681=	NG_008376.4:g.6681G>C	NG_008376.4:g.6681G>A
CYP2D6 transcript variant 1	NM_000106.6:c.408=	NM_000106.6:c.408G>C	NM_000106.6:c.408G>A
CYP2D6 transcript variant 1	NM_000106.5:c.408=	NM_000106.5:c.408G>C	NM_000106.5:c.408G>A
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1	NW_015148968.1:g.6871G>C	NW_015148968.1:g.6871=	NW_015148968.1:g.6871G>T
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1	NW_014040931.1:g.22719G>C	NW_014040931.1:g.22719=	NW_014040931.1:g.22719G>T
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1	NW_009646208.1:g.14696G>C	NW_009646208.1:g.14696=	NW_009646208.1:g.14696G>T
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1	NW_004504305.1:g.51457G>C	NW_004504305.1:g.51457=	NW_004504305.1:g.51457G>T
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1	NT_187682.1:g.51471G>C	NT_187682.1:g.51471=	NT_187682.1:g.51471G>T
GRCh37.p13 chr 22	NC_000022.10:g.42525132G>C	NC_000022.10:g.42525132=	NC_000022.10:g.42525132G>T
cytochrome P450 2D6 isoform 1	NP_000097.3:p.Val136=	NP_000097.3:p.Val136=	NP_000097.3:p.Val136=
CYP2D6 transcript variant 2	NM_001025161.2:c.353-186C>G	NM_001025161.2:c.353-186=	NM_001025161.2:c.353-186C>A
CYP2D6 transcript variant 2	NM_001025161.3:c.353-186=	NM_001025161.3:c.353-186G>C	NM_001025161.3:c.353-186G>A

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#.

77 SubSNP, 5 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1290513	Oct 10, 2002 (124)
2	LEE	ss1539430	Oct 05, 2000 (86)
3	BIOVENTURES	ss32476042	May 24, 2005 (126)
4	ABI	ss41530768	Mar 10, 2006 (126)
5	CORNELL	ss86272053	Mar 23, 2008 (147)
6	HUMANGENOME_JCVI	ss96102594	Feb 04, 2009 (130)
7	1000GENOMES	ss112671850	Feb 14, 2009 (130)
8	ENSEMBL	ss142697061	Dec 01, 2009 (131)
9	EGP_SNPS	ss159831292	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss168008143	Jul 04, 2010 (132)
11	COMPLETE_GENOMICS	ss169359463	Jul 04, 2010 (132)
12	BUSHMAN	ss204099760	Jul 04, 2010 (132)
13	1000GENOMES	ss228698358	Jul 14, 2010 (132)
14	1000GENOMES	ss238081970	Jul 15, 2010 (132)
15	1000GENOMES	ss244197293	Jul 15, 2010 (132)
16	PJP	ss292767921	May 09, 2011 (134)
17	1000GENOMES	ss491194349	May 04, 2012 (137)
18	CLINSEQ_SNP	ss491825741	May 04, 2012 (137)
19	TISHKOFF	ss566667078	Apr 25, 2013 (138)
20	SSMP	ss662596367	Apr 25, 2013 (138)
21	NHLBI-ESP	ss713628921	Apr 25, 2013 (138)
22	EVA-GONL	ss995393812	Aug 21, 2014 (142)
23	JMKIDD_LAB	ss1067607083	Aug 21, 2014 (142)
24	1000GENOMES	ss1367336156	Aug 21, 2014 (142)
25	DDI	ss1429268131	Apr 01, 2015 (144)
26	EVA_EXAC	ss1694379471	Apr 01, 2015 (144)
27	WEILL_CORNELL_DGM	ss1938961297	Feb 12, 2016 (147)
28	GENOMED	ss1969279597	Jul 19, 2016 (147)
29	JJLAB	ss2030253493	Sep 14, 2016 (149)
30	USC_VALOUEV	ss2158873719	Dec 20, 2016 (150)
31	SYSTEMSBIOZJU	ss2629622770	Nov 08, 2017 (151)
32	GRF	ss2704626602	Nov 08, 2017 (151)
33	GNOMAD	ss2745191932	Nov 08, 2017 (151)
34	GNOMAD	ss2750571758	Nov 08, 2017 (151)
35	AFFY	ss2985240509	Nov 08, 2017 (151)
36	AFFY	ss2985857673	Nov 08, 2017 (151)
37	SWEGEN	ss3019375544	Nov 08, 2017 (151)
38	BIOINF_KMB_FNS_UNIBA	ss3028962580	Nov 08, 2017 (151)
39	CSHL	ss3352855499	Nov 08, 2017 (151)
40	OMUKHERJEE_ADBS	ss3646568232	Oct 12, 2018 (152)
41	ILLUMINA	ss3654008763	Oct 12, 2018 (152)
42	EVA_DECODE	ss3708287365	Jul 13, 2019 (153)
43	ACPOP	ss3743969271	Jul 13, 2019 (153)
44	EVA	ss3759434311	Jul 13, 2019 (153)
45	EVA	ss3825454866	Apr 27, 2020 (154)
46	EVA	ss3825972714	Apr 27, 2020 (154)
47	EVA	ss3836012236	Apr 27, 2020 (154)
48	EVA	ss3841634488	Apr 27, 2020 (154)
49	SGDP_PRJ	ss3890637699	Apr 27, 2020 (154)
50	KRGDB	ss3941035025	Apr 27, 2020 (154)
51	FSA-LAB	ss3984237327	Apr 26, 2021 (155)
52	EVA	ss3986866477	Apr 26, 2021 (155)
53	VINODS	ss4034712631	Apr 26, 2021 (155)
54	VINODS	ss4034758254	Apr 26, 2021 (155)
55	TOPMED	ss5110780762	Apr 26, 2021 (155)
56	TOMMO_GENOMICS	ss5232837191	Apr 26, 2021 (155)
57	EVA	ss5236992027	Apr 26, 2021 (155)
58	EVA	ss5237618466	Apr 26, 2021 (155)
59	EVA	ss5237676623	Oct 16, 2022 (156)
60	1000G_HIGH_COVERAGE	ss5311255668	Oct 16, 2022 (156)
61	TRAN_CS_UWATERLOO	ss5314458117	Oct 16, 2022 (156)
62	EVA	ss5441587621	Oct 16, 2022 (156)
63	EVA	ss5512474024	Oct 16, 2022 (156)
64	1000G_HIGH_COVERAGE	ss5618884827	Oct 16, 2022 (156)
65	EVA	ss5623984018	Oct 16, 2022 (156)
66	EVA	ss5624123278	Oct 16, 2022 (156)
67	SANFORD_IMAGENETICS	ss5664576736	Oct 16, 2022 (156)
68	TOMMO_GENOMICS	ss5794029173	Oct 16, 2022 (156)
69	EVA	ss5799405072	Oct 16, 2022 (156)
70	EVA	ss5799469241	Oct 16, 2022 (156)
71	YY_MCH	ss5818748104	Oct 16, 2022 (156)
72	EVA	ss5822131246	Oct 16, 2022 (156)
73	EVA	ss5848570321	Oct 16, 2022 (156)
74	EVA	ss5936464916	Oct 16, 2022 (156)
75	EVA	ss5936580641	Oct 16, 2022 (156)
76	EVA	ss5959434923	Oct 16, 2022 (156)
77	EVA	ss5979638963	Oct 16, 2022 (156)
78	1000Genomes_30x	NC_000022.11 - 42129130	Oct 16, 2022 (156)
79	gnomAD - Genomes	NC_000022.11 - 42129130	Apr 26, 2021 (155)
80	14KJPN	NC_000022.11 - 42129130	Oct 16, 2022 (156)
81	TopMed	NC_000022.11 - 42129130	Apr 26, 2021 (155)
82	ALFA	NC_000022.11 - 42129130	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)
rs3892096	Dec 02, 2004 (124)
rs28371708	Mar 10, 2006 (126)
rs61736911	Jul 19, 2016 (147)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss112671850, ss168008143, ss169359463, ss204099760, ss292767921, ss491825741	NC_000022.9:40855075:G:G	NC_000022.11:42129129:C:G	(self)
ss228698358, ss238081970, ss244197293, ss491194349, ss566667078, ss662596367, ss713628921, ss995393812, ss1067607083, ss1367336156, ss1429268131, ss1694379471, ss1938961297, ss1969279597, ss2030253493, ss2158873719, ss2629622770, ss2704626602, ss2745191932, ss2750571758, ss2985240509, ss2985857673, ss3019375544, ss3352855499, ss3646568232, ss3654008763, ss3743969271, ss3759434311, ss3825454866, ss3825972714, ss3836012236, ss3841634488, ss3890637699, ss3941035025, ss3984237327, ss3986866477, ss5232837191, ss5237618466, ss5441587621, ss5512474024, ss5623984018, ss5624123278, ss5664576736, ss5799405072, ss5799469241, ss5822131246, ss5848570321, ss5936464916, ss5936580641, ss5959434923, ss5979638963	NC_000022.10:42525131:G:G	NC_000022.11:42129129:C:G	(self)
106410762, 571270046, 127866277, 385889709, 12201294190, ss3028962580, ss3708287365, ss5110780762, ss5236992027, ss5237676623, ss5311255668, ss5314458117, ss5618884827, ss5794029173, ss5818748104	NC_000022.11:42129129:C:G	NC_000022.11:42129129:C:G	(self)
ss1290513, ss1539430, ss32476042, ss41530768, ss86272053, ss96102594, ss142697061, ss159831292	NT_011520.12:21915700:G:G	NC_000022.11:42129129:C:G	(self)
ss4034758254	NT_187682.1:51470:G:G	NC_000022.11:42129129:C:G	(self)
ss4034712631	NW_004504305.1:51456:G:G	NC_000022.11:42129129:C:G	(self)
ss5512474024	NC_000022.10:42525131:G:T	NC_000022.11:42129129:C:T

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

15 citations for rs1058164

PMID	Title	Author	Year	Journal
18698231	Polymorphisms affecting gene transcription and mRNA processing in pharmacogenetic candidate genes: detection through allelic expression imbalance in human target tissues.	Johnson AD et al.	2008	Pharmacogenetics and genomics
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
21790905	CYP2B6 SNPs are associated with methadone dose required for effective treatment of opioid addiction.	Levran O et al.	2013	Addiction biology
23133420	Pharmacogenomic Diversity among Brazilians: Influence of Ancestry, Self-Reported Color, and Geographical Origin.	Suarez-Kurtz G et al.	2012	Frontiers in pharmacology
24798984	Developing and Evaluating the HRM Technique for Identifying Cytochrome P450 2D6 Polymorphisms.	Lu HC et al.	2015	Journal of clinical laboratory analysis
24944790	Screening for 392 polymorphisms in 141 pharmacogenes.	Kim JY et al.	2014	Biomedical reports
26858644	Cross-Comparison of Exome Analysis, Next-Generation Sequencing of Amplicons, and the iPLEX(®) ADME PGx Panel for Pharmacogenomic Profiling.	Chua EW et al.	2016	Frontiers in pharmacology
27110117	Clinically relevant genetic variants of drug-metabolizing enzyme and transporter genes detected in Thai children and adolescents with autism spectrum disorder.	Medhasi S et al.	2016	Neuropsychiatric disease and treatment
27228982	Genetic polymorphisms analysis of CYP2D6 in the Uygur population.	He X et al.	2016	BMC genomics
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
31019283	Secondary actionable findings identified by exome sequencing: expected impact on the organisation of care from the study of 700 consecutive tests.	Thauvin-Robinet C et al.	2019	European journal of human genetics
33586456	Influence of CYP2D6 gene polymorphisms on the pharmacokinetics of aripiprazole in healthy Chinese subjects.	Zhang X et al.	2021	Pharmacogenomics
34621706	Comprehensive analysis of important pharmacogenes in Koreans using the DMET™ platform.	Kim B et al.	2021	Translational and clinical pharmacology
34823523	Prediction of the CYP2D6 enzymatic activity based on investigating of the CYP2D6 genotypes around the vivax malaria patients in Yunnan Province, China.	Dong Y et al.	2021	Malaria journal
36013302	From Croatian Roma to 1000 Genomes: The Story of the CYP2D6 Gene Promoter and Enhancer SNPs.	Stojanović Marković A et al.	2022	Journal of personalized medicine

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
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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

rs1058164