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dbSNP Short Genetic Variations

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.

rs267608319

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr22:42126749 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000616 (163/264690, TOPMED)
T=0.000219 (32/145816, GnomAD_exome)
T=0.000369 (51/138240, GnomAD) (+ 5 more)
T=0.00004 (1/28206, 14KJPN)
T=0.00034 (8/23408, ALFA)
T=0.00020 (3/15082, ExAC)
T=0.0012 (8/6404, 1000G_30x)
T=0.0012 (6/5008, 1000G)
Clinical Significance
Reported in ClinVar
Gene : Consequence
CYP2D6 : Missense Variant
Publications
4 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 23408 C=0.99966 T=0.00034
European Sub 15886 C=0.99962 T=0.00038
African Sub 3540 C=0.9997 T=0.0003
African Others Sub 122 C=1.000 T=0.000
African American Sub 3418 C=0.9997 T=0.0003
Asian Sub 168 C=1.000 T=0.000
East Asian Sub 112 C=1.000 T=0.000
Other Asian Sub 56 C=1.00 T=0.00
Latin American 1 Sub 146 C=1.000 T=0.000
Latin American 2 Sub 610 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 2960 C=0.9997 T=0.0003


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.999384 T=0.000616
gnomAD - Exomes Global Study-wide 145816 C=0.999781 T=0.000219
gnomAD - Exomes European Sub 70012 C=0.99980 T=0.00020
gnomAD - Exomes Asian Sub 32896 C=0.99997 T=0.00003
gnomAD - Exomes American Sub 23474 C=0.99945 T=0.00055
gnomAD - Exomes Ashkenazi Jewish Sub 7938 C=1.0000 T=0.0000
gnomAD - Exomes African Sub 7372 C=0.9997 T=0.0003
gnomAD - Exomes Other Sub 4124 C=0.9995 T=0.0005
gnomAD - Genomes Global Study-wide 138240 C=0.999631 T=0.000369
gnomAD - Genomes European Sub 75338 C=0.99983 T=0.00017
gnomAD - Genomes African Sub 40876 C=0.99983 T=0.00017
gnomAD - Genomes American Sub 13494 C=0.99785 T=0.00215
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3102 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2110 C=0.9991 T=0.0009
14KJPN JAPANESE Study-wide 28206 C=0.99996 T=0.00004
Allele Frequency Aggregator Total Global 23408 C=0.99966 T=0.00034
Allele Frequency Aggregator European Sub 15886 C=0.99962 T=0.00038
Allele Frequency Aggregator African Sub 3540 C=0.9997 T=0.0003
Allele Frequency Aggregator Other Sub 2960 C=0.9997 T=0.0003
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 168 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
ExAC Global Study-wide 15082 C=0.99980 T=0.00020
ExAC Asian Sub 6946 C=0.9999 T=0.0001
ExAC Europe Sub 6162 C=0.9997 T=0.0003
ExAC African Sub 1420 C=1.0000 T=0.0000
ExAC American Sub 384 C=1.000 T=0.000
ExAC Other Sub 170 C=1.000 T=0.000
1000Genomes_30x Global Study-wide 6404 C=0.9988 T=0.0012
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=0.9976 T=0.0024
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=0.995 T=0.005
1000Genomes Global Study-wide 5008 C=0.9988 T=0.0012
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9980 T=0.0020
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=0.994 T=0.006
Help

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.42126749C>T
CYP2D6 RefSeqGene (LRG_303) NG_008376.4:g.9062G>A
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1 NW_015148968.1:g.4490C>T
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1 NW_014040931.1:g.20338C>T
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1 NW_009646208.1:g.12315C>T
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1 NW_004504305.1:g.49076C>T
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1 NT_187682.1:g.49090C>T
GRCh37.p13 chr 22 NC_000022.10:g.42522751C>T
Gene: CYP2D6, cytochrome P450 family 2 subfamily D member 6 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
CYP2D6 transcript variant 1 NM_000106.6:c.1319G>A R [CGC] > H [CAC] Coding Sequence Variant
cytochrome P450 2D6 isoform 1 NP_000097.3:p.Arg440His R (Arg) > H (His) Missense Variant
CYP2D6 transcript variant 2 NM_001025161.3:c.1166G>A R [CGC] > H [CAC] Coding Sequence Variant
cytochrome P450 2D6 isoform 2 NP_001020332.2:p.Arg389His R (Arg) > H (His) Missense Variant
Help

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: T (allele ID: 181380 )
ClinVar Accession Disease Names Clinical Significance
RCV000162080.2 not provided Drug-Response
Help

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= T
GRCh38.p14 chr 22 NC_000022.11:g.42126749= NC_000022.11:g.42126749C>T
CYP2D6 RefSeqGene (LRG_303) NG_008376.4:g.9062= NG_008376.4:g.9062G>A
CYP2D6 transcript variant 1 NM_000106.6:c.1319= NM_000106.6:c.1319G>A
CYP2D6 transcript variant 1 NM_000106.5:c.1319= NM_000106.5:c.1319G>A
CYP2D6 transcript variant 2 NM_001025161.3:c.1166= NM_001025161.3:c.1166G>A
CYP2D6 transcript variant 2 NM_001025161.2:c.1166= NM_001025161.2:c.1166G>A
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1 NW_015148968.1:g.4490= NW_015148968.1:g.4490C>T
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1 NW_014040931.1:g.20338= NW_014040931.1:g.20338C>T
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1 NW_009646208.1:g.12315= NW_009646208.1:g.12315C>T
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1 NW_004504305.1:g.49076= NW_004504305.1:g.49076C>T
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1 NT_187682.1:g.49090= NT_187682.1:g.49090C>T
GRCh37.p13 chr 22 NC_000022.10:g.42522751= NC_000022.10:g.42522751C>T
cytochrome P450 2D6 isoform 1 NP_000097.3:p.Arg440= NP_000097.3:p.Arg440His
cytochrome P450 2D6 isoform 2 NP_001020332.2:p.Arg389= NP_001020332.2:p.Arg389His
Help

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#.

16 SubSNP, 8 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CMH_GENOMICS ss538296140 Aug 08, 2012 (137)
2 1000GENOMES ss1367336002 Aug 21, 2014 (142)
3 EVA_EXAC ss1694378935 Apr 01, 2015 (144)
4 CMH_GENOMICS ss1712297599 Mar 11, 2015 (142)
5 CLINVAR ss1713612541 Mar 12, 2015 (142)
6 GNOMAD ss2745191201 Nov 08, 2017 (151)
7 GNOMAD ss2750571490 Nov 08, 2017 (151)
8 GNOMAD ss2974893275 Nov 08, 2017 (151)
9 TOPMED ss5110779723 Apr 26, 2021 (155)
10 1000G_HIGH_COVERAGE ss5311255520 Oct 16, 2022 (156)
11 TRAN_CS_UWATERLOO ss5314458115 Oct 16, 2022 (156)
12 EVA ss5441587407 Oct 16, 2022 (156)
13 EVA ss5512473982 Oct 16, 2022 (156)
14 1000G_HIGH_COVERAGE ss5618884613 Oct 16, 2022 (156)
15 SANFORD_IMAGENETICS ss5664576640 Oct 16, 2022 (156)
16 TOMMO_GENOMICS ss5794028918 Oct 16, 2022 (156)
17 1000Genomes NC_000022.10 - 42522751 Oct 12, 2018 (152)
18 1000Genomes_30x NC_000022.11 - 42126749 Oct 16, 2022 (156)
19 ExAC NC_000022.10 - 42522751 Oct 12, 2018 (152)
20 gnomAD - Genomes NC_000022.11 - 42126749 Apr 26, 2021 (155)
21 gnomAD - Exomes NC_000022.10 - 42522751 Jul 13, 2019 (153)
22 14KJPN NC_000022.11 - 42126749 Oct 16, 2022 (156)
23 TopMed NC_000022.11 - 42126749 Apr 26, 2021 (155)
24 ALFA NC_000022.11 - 42126749 Apr 26, 2021 (155)
25 ClinVar RCV000162080.2 Oct 16, 2022 (156)
Help

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
80894416, 5962208, 14523953, ss1367336002, ss1694378935, ss2745191201, ss2750571490, ss2974893275, ss5441587407, ss5512473982, ss5664576640 NC_000022.10:42522750:C:T NC_000022.11:42126748:C:T (self)
RCV000162080.2, 106410548, 571269168, 127866022, 385888670, 760269872, ss1712297599, ss1713612541, ss5110779723, ss5311255520, ss5314458115, ss5618884613, ss5794028918 NC_000022.11:42126748:C:T NC_000022.11:42126748:C:T (self)
ss538296140 NT_011520.12:21913319:C:T NC_000022.11:42126748:C:T (self)
Help

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

4 citations for rs267608319
PMID Title Author Year Journal
9241659 Polymorphism of the cytochrome P450 CYP2D6 gene in a European population: characterization of 48 mutations and 53 alleles, their frequencies and evolution. Marez D et al. 1997 Pharmacogenetics
15726636 Functional analysis of CYP2D6.31 variant: homology modeling suggests possible disruption of redox partner interaction by Arg440His substitution. Allorge D et al. 2005 Proteins
17460029 A natural variant of the heme-binding signature (R441C) resulting in complete loss of function of CYP2D6. Klein K et al. 2007 Drug metabolism and disposition
20473659 Discovery of the nonfunctional CYP2D6 31 allele in Spanish, Puerto Rican, and US Hispanic populations. Gaedigk A et al. 2010 European journal of clinical pharmacology
Help

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.

Software version is: 2.0.1.post761+d5e8e07