Name: rs1135822
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.

rs1135822

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:42129180 (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 / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000907 (240/264690, TOPMED)
T=0.000437 (61/139508, GnomAD)
T=0.001376 (155/112640, ExAC) (+ 6 more)
T=0.00038 (16/42250, ALFA)
T=0.00678 (191/28168, 14KJPN)
T=0.00754 (126/16714, 8.3KJPN)
T=0.00024 (3/12394, GO-ESP)
T=0.0016 (10/6404, 1000G_30x)
T=0.0178 (52/2916, KOREAN)

Clinical Significance: Reported in ClinVar
Gene : Consequence: CYP2D6 : Missense Variant
LOC102723722 : 2KB Upstream Variant
Publications: 2 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	42250	A=0.99962	T=0.00038	0.99929	4.7e-05	0.000663	32
European	Sub	30446	A=0.99974	T=0.00026	0.999474	0.0	0.000526	0
African	Sub	3476	A=0.9997	T=0.0003	0.999425	0.0	0.000575	0
African Others	Sub	116	A=1.000	T=0.000	1.0	0.0	0.0	N/A
African American	Sub	3360	A=0.9997	T=0.0003	0.999405	0.0	0.000595	0
Asian	Sub	164	A=0.976	T=0.024	0.963415	0.012195	0.02439	11
East Asian	Sub	110	A=0.982	T=0.018	0.981818	0.018182	0.0	29
Other Asian	Sub	54	A=0.96	T=0.04	0.925926	0.0	0.074074	0
Latin American 1	Sub	492	A=1.000	T=0.000	1.0	0.0	0.0	N/A
Latin American 2	Sub	628	A=1.000	T=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	94	A=1.00	T=0.00	1.0	0.0	0.0	N/A
Other	Sub	6950	A=0.9996	T=0.0004	0.999137	0.0	0.000863	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	A=0.999093	T=0.000907
gnomAD - Genomes	Global	Study-wide	139508	A=0.999563	T=0.000437
gnomAD - Genomes	European	Sub	75684	A=0.99987	T=0.00013
gnomAD - Genomes	African	Sub	41620	A=0.99986	T=0.00014
gnomAD - Genomes	American	Sub	13618	A=0.99868	T=0.00132
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=1.0000	T=0.0000
gnomAD - Genomes	East Asian	Sub	3120	A=0.9917	T=0.0083
gnomAD - Genomes	Other	Sub	2142	A=0.9995	T=0.0005
ExAC	Global	Study-wide	112640	A=0.998624	T=0.001376
ExAC	Europe	Sub	68194	A=0.99985	T=0.00015
ExAC	Asian	Sub	24232	A=0.99624	T=0.00376
ExAC	American	Sub	11030	A=0.99538	T=0.00462
ExAC	African	Sub	8348	A=0.9996	T=0.0004
ExAC	Other	Sub	836	A=1.000	T=0.000
Allele Frequency Aggregator	Total	Global	42250	A=0.99962	T=0.00038
Allele Frequency Aggregator	European	Sub	30446	A=0.99974	T=0.00026
Allele Frequency Aggregator	Other	Sub	6950	A=0.9996	T=0.0004
Allele Frequency Aggregator	African	Sub	3476	A=0.9997	T=0.0003
Allele Frequency Aggregator	Latin American 2	Sub	628	A=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	492	A=1.000	T=0.000
Allele Frequency Aggregator	Asian	Sub	164	A=0.976	T=0.024
Allele Frequency Aggregator	South Asian	Sub	94	A=1.00	T=0.00
14KJPN	JAPANESE	Study-wide	28168	A=0.99322	T=0.00678
8.3KJPN	JAPANESE	Study-wide	16714	A=0.99246	T=0.00754
GO Exome Sequencing Project	Global	Study-wide	12394	A=0.99976	T=0.00024
GO Exome Sequencing Project	European American	Sub	8336	A=0.9999	T=0.0001
GO Exome Sequencing Project	African American	Sub	4058	A=0.9995	T=0.0005
1000Genomes_30x	Global	Study-wide	6404	A=0.9984	T=0.0016
1000Genomes_30x	African	Sub	1786	A=1.0000	T=0.0000
1000Genomes_30x	Europe	Sub	1266	A=1.0000	T=0.0000
1000Genomes_30x	South Asian	Sub	1202	A=1.0000	T=0.0000
1000Genomes_30x	East Asian	Sub	1170	A=0.9915	T=0.0085
1000Genomes_30x	American	Sub	980	A=1.000	T=0.000
KOREAN population from KRGDB	KOREAN	Study-wide	2916	A=0.9822	T=0.0178

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.42129180A>G
GRCh38.p14 chr 22	NC_000022.11:g.42129180A>T
gene/pseudogene RefSeqGene (LRG_303)	NG_008376.4:g.6631T>C
gene/pseudogene RefSeqGene (LRG_303)	NG_008376.4:g.6631T>A
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1	NW_015148968.1:g.6921A>G
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1	NW_015148968.1:g.6921A>T
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1	NW_014040931.1:g.22769A>G
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1	NW_014040931.1:g.22769A>T
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1	NW_009646208.1:g.14746A>G
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1	NW_009646208.1:g.14746A>T
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1	NW_004504305.1:g.51507A>G
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1	NW_004504305.1:g.51507A>T
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1	NT_187682.1:g.51521A>G
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1	NT_187682.1:g.51521A>T
GRCh37.p13 chr 22	NC_000022.10:g.42525182A>G
GRCh37.p13 chr 22	NC_000022.10:g.42525182A>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.353-236T… NM_001025161.3:c.353-236T>C	N/A	Intron Variant
CYP2D6 transcript variant 1	NM_000106.6:c.358T>C	F [TTC] > L [CTC]	Coding Sequence Variant
cytochrome P450 2D6 isoform 1	NP_000097.3:p.Phe120Leu	F (Phe) > L (Leu)	Missense Variant
CYP2D6 transcript variant 1	NM_000106.6:c.358T>A	F [TTC] > I [ATC]	Coding Sequence Variant
cytochrome P450 2D6 isoform 1	NP_000097.3:p.Phe120Ile	F (Phe) > I (Ile)	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: 818001 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001029591.2	Tramadol response	Drug-Response

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	T
GRCh38.p14 chr 22	NC_000022.11:g.42129180=	NC_000022.11:g.42129180A>G	NC_000022.11:g.42129180A>T
gene/pseudogene RefSeqGene (LRG_303)	NG_008376.4:g.6631=	NG_008376.4:g.6631T>C	NG_008376.4:g.6631T>A
CYP2D6 transcript variant 1	NM_000106.6:c.358=	NM_000106.6:c.358T>C	NM_000106.6:c.358T>A
CYP2D6 transcript variant 1	NM_000106.5:c.358=	NM_000106.5:c.358T>C	NM_000106.5:c.358T>A
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1	NW_015148968.1:g.6921=	NW_015148968.1:g.6921A>G	NW_015148968.1:g.6921A>T
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1	NW_014040931.1:g.22769=	NW_014040931.1:g.22769A>G	NW_014040931.1:g.22769A>T
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1	NW_009646208.1:g.14746=	NW_009646208.1:g.14746A>G	NW_009646208.1:g.14746A>T
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1	NW_004504305.1:g.51507=	NW_004504305.1:g.51507A>G	NW_004504305.1:g.51507A>T
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1	NT_187682.1:g.51521=	NT_187682.1:g.51521A>G	NT_187682.1:g.51521A>T
GRCh37.p13 chr 22	NC_000022.10:g.42525182=	NC_000022.10:g.42525182A>G	NC_000022.10:g.42525182A>T
cytochrome P450 2D6 isoform 1	NP_000097.3:p.Phe120=	NP_000097.3:p.Phe120Leu	NP_000097.3:p.Phe120Ile
CYP2D6 transcript variant 2	NM_001025161.2:c.353-236=	NM_001025161.2:c.353-236T>C	NM_001025161.2:c.353-236T>A
CYP2D6 transcript variant 2	NM_001025161.3:c.353-236=	NM_001025161.3:c.353-236T>C	NM_001025161.3:c.353-236T>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#.

37 SubSNP, 11 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	BIOVENTURES	ss32476041	May 24, 2005 (126)
2	EXOME_CHIP	ss491572624	May 04, 2012 (137)
3	CLINSEQ_SNP	ss491825743	May 04, 2012 (137)
4	NHLBI-ESP	ss713628930	Apr 25, 2013 (138)
5	ILLUMINA	ss783469992	Aug 21, 2014 (142)
6	EVA_EXAC	ss1694379501	Apr 01, 2015 (144)
7	ILLUMINA	ss1946595229	Feb 12, 2016 (147)
8	ILLUMINA	ss2633883903	Nov 08, 2017 (151)
9	GRF	ss2704626603	Nov 08, 2017 (151)
10	ILLUMINA	ss2710959492	Nov 08, 2017 (151)
11	GNOMAD	ss2745191960	Nov 08, 2017 (151)
12	GNOMAD	ss2750571773	Nov 08, 2017 (151)
13	GNOMAD	ss2974893707	Nov 08, 2017 (151)
14	SWEGEN	ss3019375548	Nov 08, 2017 (151)
15	ILLUMINA	ss3022190904	Nov 08, 2017 (151)
16	ILLUMINA	ss3628544574	Oct 12, 2018 (152)
17	ILLUMINA	ss3634870366	Oct 12, 2018 (152)
18	ILLUMINA	ss3640577669	Oct 12, 2018 (152)
19	ILLUMINA	ss3652655256	Oct 12, 2018 (152)
20	ILLUMINA	ss3745170209	Jul 13, 2019 (153)
21	EVA	ss3825454874	Apr 27, 2020 (154)
22	KRGDB	ss3941035030	Apr 27, 2020 (154)
23	TOPMED	ss5110780799	Apr 26, 2021 (155)
24	TOMMO_GENOMICS	ss5232837195	Apr 26, 2021 (155)
25	1000G_HIGH_COVERAGE	ss5311255673	Oct 16, 2022 (156)
26	TRAN_CS_UWATERLOO	ss5314458119	Oct 16, 2022 (156)
27	EVA	ss5441587630	Oct 16, 2022 (156)
28	HUGCELL_USP	ss5503082691	Oct 16, 2022 (156)
29	EVA	ss5512474026	Oct 16, 2022 (156)
30	1000G_HIGH_COVERAGE	ss5618884833	Oct 16, 2022 (156)
31	TOMMO_GENOMICS	ss5794029177	Oct 16, 2022 (156)
32	EVA	ss5799405076	Oct 16, 2022 (156)
33	YY_MCH	ss5818748105	Oct 16, 2022 (156)
34	EVA	ss5847946439	Oct 16, 2022 (156)
35	EVA	ss5936464938	Oct 16, 2022 (156)
36	EVA	ss5959434926	Oct 16, 2022 (156)
37	EVA	ss5979638966	Oct 16, 2022 (156)
38	1000Genomes_30x	NC_000022.11 - 42129180	Oct 16, 2022 (156)
39	ExAC	NC_000022.10 - 42525182	Oct 12, 2018 (152)
40	gnomAD - Genomes	NC_000022.11 - 42129180	Apr 26, 2021 (155)
41	gnomAD - Exomes Submission ignored due to conflicting rows: Row 14524753 (NC_000022.10:42525181:A:A 239356/239358, NC_000022.10:42525181:A:G 2/239358) Row 14524754 (NC_000022.10:42525181:A:A 238962/239358, NC_000022.10:42525181:A:T 396/239358)	-	Jul 13, 2019 (153)
42	gnomAD - Exomes Submission ignored due to conflicting rows: Row 14524753 (NC_000022.10:42525181:A:A 239356/239358, NC_000022.10:42525181:A:G 2/239358) Row 14524754 (NC_000022.10:42525181:A:A 238962/239358, NC_000022.10:42525181:A:T 396/239358)	-	Jul 13, 2019 (153)
43	GO Exome Sequencing Project	NC_000022.10 - 42525182	Oct 12, 2018 (152)
44	KOREAN population from KRGDB	NC_000022.10 - 42525182	Apr 27, 2020 (154)
45	8.3KJPN	NC_000022.10 - 42525182	Apr 26, 2021 (155)
46	14KJPN	NC_000022.11 - 42129180	Oct 16, 2022 (156)
47	TopMed	NC_000022.11 - 42129180	Apr 26, 2021 (155)
48	ALFA	NC_000022.11 - 42129180	Apr 26, 2021 (155)
49	ClinVar	RCV001029591.2	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)
rs17362176	Mar 11, 2006 (126)
rs28371707	Mar 11, 2006 (126)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss2745191960	NC_000022.10:42525181:A:G	NC_000022.11:42129179:A:G	(self)
RCV001029591.2	NC_000022.11:42129179:A:G	NC_000022.11:42129179:A:G	(self)
ss491825743	NC_000022.9:40855125:A:T	NC_000022.11:42129179:A:T	(self)
5962821, 1911703, 48212424, 90806502, ss491572624, ss713628930, ss783469992, ss1694379501, ss1946595229, ss2633883903, ss2704626603, ss2710959492, ss2745191960, ss2750571773, ss2974893707, ss3019375548, ss3022190904, ss3628544574, ss3634870366, ss3640577669, ss3652655256, ss3745170209, ss3825454874, ss3941035030, ss5232837195, ss5441587630, ss5512474026, ss5799405076, ss5847946439, ss5936464938, ss5959434926, ss5979638966	NC_000022.10:42525181:A:T	NC_000022.11:42129179:A:T	(self)
106410768, 571270076, 127866281, 385889746, 5198964240, ss5110780799, ss5311255673, ss5314458119, ss5503082691, ss5618884833, ss5794029177, ss5818748105	NC_000022.11:42129179:A:T	NC_000022.11:42129179:A:T	(self)
ss32476041	NT_011520.12:21915750:A:T	NC_000022.11:42129179:A:T	(self)

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

2 citations for rs1135822

PMID	Title	Author	Year	Journal
24944790	Screening for 392 polymorphisms in 141 pharmacogenes.	Kim JY et al.	2014	Biomedical reports
27108086	Multiplex SNaPshot-a new simple and efficient CYP2D6 and ADRB1 genotyping method.	Ben S et al.	2016	Human genomics

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

rs1135822