Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs78482768

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr22:42129087 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.002731 (723/264690, TOPMED)
C=0.002393 (586/244856, GnomAD_exome)
C=0.002499 (349/139680, GnomAD) (+ 6 more)
C=0.002392 (247/103244, ExAC)
C=0.00213 (105/49216, ALFA)
C=0.00264 (33/12514, GO-ESP)
C=0.0011 (7/6404, 1000G_30x)
C=0.0012 (6/5008, 1000G)
C=0.007 (4/534, MGP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CYP2D6 : Stop Gained
LOC102723722 : 2KB Upstream Variant
Publications
1 citation
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 49216 G=0.99787 A=0.00000, C=0.00213 0.995814 8.1e-05 0.004104 17
European Sub 37206 G=0.99785 A=0.00000, C=0.00215 0.995807 0.000108 0.004085 23
African Sub 3570 G=1.0000 A=0.0000, C=0.0000 1.0 0.0 0.0 N/A
African Others Sub 122 G=1.000 A=0.000, C=0.000 1.0 0.0 0.0 N/A
African American Sub 3448 G=1.0000 A=0.0000, C=0.0000 1.0 0.0 0.0 N/A
Asian Sub 168 G=1.000 A=0.000, C=0.000 1.0 0.0 0.0 N/A
East Asian Sub 112 G=1.000 A=0.000, C=0.000 1.0 0.0 0.0 N/A
Other Asian Sub 56 G=1.00 A=0.00, C=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 500 G=0.990 A=0.000, C=0.010 0.98 0.0 0.02 0
Latin American 2 Sub 624 G=1.000 A=0.000, C=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 G=1.00 A=0.00, C=0.00 1.0 0.0 0.0 N/A
Other Sub 7050 G=0.9972 A=0.0000, C=0.0028 0.994326 0.0 0.005674 0


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 G=0.997269 C=0.002731
gnomAD - Exomes Global Study-wide 244856 G=0.997607 C=0.002393
gnomAD - Exomes European Sub 131878 G=0.997278 C=0.002722
gnomAD - Exomes Asian Sub 48222 G=0.99971 C=0.00029
gnomAD - Exomes American Sub 34146 G=0.99476 C=0.00524
gnomAD - Exomes African Sub 14716 G=0.99912 C=0.00088
gnomAD - Exomes Ashkenazi Jewish Sub 9958 G=0.9994 C=0.0006
gnomAD - Exomes Other Sub 5936 G=0.9975 C=0.0025
gnomAD - Genomes Global Study-wide 139680 G=0.997501 C=0.002499
gnomAD - Genomes European Sub 75754 G=0.99695 C=0.00305
gnomAD - Genomes African Sub 41710 G=0.99930 C=0.00070
gnomAD - Genomes American Sub 13626 G=0.99486 C=0.00514
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9982 C=0.0018
gnomAD - Genomes East Asian Sub 3122 G=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2144 G=0.9939 C=0.0061
ExAC Global Study-wide 103244 G=0.997608 C=0.002392
ExAC Europe Sub 62302 G=0.99705 C=0.00295
ExAC Asian Sub 22822 G=0.99965 C=0.00035
ExAC American Sub 9932 G=0.9955 C=0.0045
ExAC African Sub 7438 G=0.9989 C=0.0011
ExAC Other Sub 750 G=0.997 C=0.003
Allele Frequency Aggregator Total Global 49216 G=0.99787 A=0.00000, C=0.00213
Allele Frequency Aggregator European Sub 37206 G=0.99785 A=0.00000, C=0.00215
Allele Frequency Aggregator Other Sub 7050 G=0.9972 A=0.0000, C=0.0028
Allele Frequency Aggregator African Sub 3570 G=1.0000 A=0.0000, C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 624 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 G=0.990 A=0.000, C=0.010
Allele Frequency Aggregator Asian Sub 168 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00, C=0.00
GO Exome Sequencing Project Global Study-wide 12514 G=0.99736 C=0.00264
GO Exome Sequencing Project European American Sub 8378 G=0.9967 C=0.0033
GO Exome Sequencing Project African American Sub 4136 G=0.9988 C=0.0012
1000Genomes_30x Global Study-wide 6404 G=0.9989 C=0.0011
1000Genomes_30x African Sub 1786 G=1.0000 C=0.0000
1000Genomes_30x Europe Sub 1266 G=0.9953 C=0.0047
1000Genomes_30x South Asian Sub 1202 G=1.0000 C=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 C=0.0000
1000Genomes_30x American Sub 980 G=0.999 C=0.001
1000Genomes Global Study-wide 5008 G=0.9988 C=0.0012
1000Genomes African Sub 1322 G=1.0000 C=0.0000
1000Genomes East Asian Sub 1008 G=1.0000 C=0.0000
1000Genomes Europe Sub 1006 G=0.9950 C=0.0050
1000Genomes South Asian Sub 978 G=1.000 C=0.000
1000Genomes American Sub 694 G=0.999 C=0.001
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.993 C=0.007
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.42129087G>A
GRCh38.p14 chr 22 NC_000022.11:g.42129087G>C
gene/pseudogene RefSeqGene (LRG_303) NG_008376.4:g.6724C>T
gene/pseudogene RefSeqGene (LRG_303) NG_008376.4:g.6724C>G
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1 NW_015148968.1:g.6828G>A
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1 NW_015148968.1:g.6828G>C
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1 NW_014040931.1:g.22676G>A
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1 NW_014040931.1:g.22676G>C
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1 NW_009646208.1:g.14653G>A
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1 NW_009646208.1:g.14653G>C
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1 NW_004504305.1:g.51414G>A
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1 NW_004504305.1:g.51414G>C
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1 NT_187682.1:g.51428G>A
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1 NT_187682.1:g.51428G>C
GRCh37.p13 chr 22 NC_000022.10:g.42525089G>A
GRCh37.p13 chr 22 NC_000022.10:g.42525089G>C
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.353-143C…

NM_001025161.3:c.353-143C>T

 		N/A Intron Variant
CYP2D6 transcript variant 1 NM_000106.6:c.451C>T Q [CAG] > * [TAG] Coding Sequence Variant
cytochrome P450 2D6 isoform 1 NP_000097.3:p.Gln151Ter Q (Gln) > * (Ter) Stop Gained
CYP2D6 transcript variant 1 NM_000106.6:c.451C>G Q [CAG] > E [GAG] Coding Sequence Variant
cytochrome P450 2D6 isoform 1 NP_000097.3:p.Gln151Glu Q (Gln) > E (Glu) 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.

Not Reported in ClinVar
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 G= A C
GRCh38.p14 chr 22 NC_000022.11:g.42129087= NC_000022.11:g.42129087G>A NC_000022.11:g.42129087G>C
gene/pseudogene RefSeqGene (LRG_303) NG_008376.4:g.6724= NG_008376.4:g.6724C>T NG_008376.4:g.6724C>G
CYP2D6 transcript variant 1 NM_000106.6:c.451= NM_000106.6:c.451C>T NM_000106.6:c.451C>G
CYP2D6 transcript variant 1 NM_000106.5:c.451= NM_000106.5:c.451C>T NM_000106.5:c.451C>G
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1 NW_015148968.1:g.6828= NW_015148968.1:g.6828G>A NW_015148968.1:g.6828G>C
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1 NW_014040931.1:g.22676= NW_014040931.1:g.22676G>A NW_014040931.1:g.22676G>C
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1 NW_009646208.1:g.14653= NW_009646208.1:g.14653G>A NW_009646208.1:g.14653G>C
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1 NW_004504305.1:g.51414= NW_004504305.1:g.51414G>A NW_004504305.1:g.51414G>C
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1 NT_187682.1:g.51428= NT_187682.1:g.51428G>A NT_187682.1:g.51428G>C
GRCh37.p13 chr 22 NC_000022.10:g.42525089= NC_000022.10:g.42525089G>A NC_000022.10:g.42525089G>C
cytochrome P450 2D6 isoform 1 NP_000097.3:p.Gln151= NP_000097.3:p.Gln151Ter NP_000097.3:p.Gln151Glu
CYP2D6 transcript variant 2 NM_001025161.2:c.353-143= NM_001025161.2:c.353-143C>T NM_001025161.2:c.353-143C>G
CYP2D6 transcript variant 2 NM_001025161.3:c.353-143= NM_001025161.3:c.353-143C>T NM_001025161.3:c.353-143C>G
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#.

28 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 RWHITE ss141047260 Dec 01, 2009 (131)
2 EGP_SNPS ss159831293 Dec 01, 2009 (131)
3 BL ss255929812 May 09, 2011 (134)
4 EXOME_CHIP ss491572622 May 04, 2012 (137)
5 NHLBI-ESP ss713628918 Apr 25, 2013 (138)
6 JMKIDD_LAB ss1067607082 Aug 21, 2014 (142)
7 1000GENOMES ss1367336153 Aug 21, 2014 (142)
8 EVA_EXAC ss1694379460 Apr 01, 2015 (144)
9 EVA_DECODE ss1699465075 Apr 01, 2015 (144)
10 EVA_MGP ss1711571587 Apr 01, 2015 (144)
11 JJLAB ss2030253492 Sep 14, 2016 (149)
12 GNOMAD ss2745191911 Nov 08, 2017 (151)
13 GNOMAD ss2750571750 Nov 08, 2017 (151)
14 GNOMAD ss2974893684 Nov 08, 2017 (151)
15 AFFY ss2985240508 Nov 08, 2017 (151)
16 AFFY ss2985857672 Nov 08, 2017 (151)
17 SWEGEN ss3019375542 Nov 08, 2017 (151)
18 ILLUMINA ss3654008762 Oct 12, 2018 (152)
19 EVA ss3825454863 Apr 27, 2020 (154)
20 EVA ss3986866476 Apr 26, 2021 (155)
21 TOPMED ss5110780742 Apr 26, 2021 (155)
22 1000G_HIGH_COVERAGE ss5311255667 Oct 16, 2022 (156)
23 EVA ss5441587618 Oct 16, 2022 (156)
24 HUGCELL_USP ss5503082687 Oct 16, 2022 (156)
25 EVA ss5512474023 Oct 16, 2022 (156)
26 1000G_HIGH_COVERAGE ss5618884823 Oct 16, 2022 (156)
27 EVA ss5848570320 Oct 16, 2022 (156)
28 EVA ss5936464903 Oct 16, 2022 (156)
29 1000Genomes NC_000022.10 - 42525089 Oct 12, 2018 (152)
30 1000Genomes_30x NC_000022.11 - 42129087 Oct 16, 2022 (156)
31 ExAC NC_000022.10 - 42525089 Oct 12, 2018 (152)
32 gnomAD - Genomes NC_000022.11 - 42129087 Apr 26, 2021 (155)
33 gnomAD - Exomes NC_000022.10 - 42525089 Jul 13, 2019 (153)
34 GO Exome Sequencing Project NC_000022.10 - 42525089 Oct 12, 2018 (152)
35 Medical Genome Project healthy controls from Spanish population NC_000022.10 - 42525089 Apr 27, 2020 (154)
36 TopMed NC_000022.11 - 42129087 Apr 26, 2021 (155)
37 ALFA NC_000022.11 - 42129087 Apr 26, 2021 (155)
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
ss5936464903 NC_000022.10:42525088:G:A NC_000022.11:42129086:G:A
9486241505 NC_000022.11:42129086:G:A NC_000022.11:42129086:G:A (self)
ss255929812, ss1699465075 NC_000022.9:40855032:G:C NC_000022.11:42129086:G:C (self)
80894573, 5962779, 14524694, 1911692, 687347, ss491572622, ss713628918, ss1067607082, ss1367336153, ss1694379460, ss1711571587, ss2030253492, ss2745191911, ss2750571750, ss2974893684, ss2985240508, ss2985857672, ss3019375542, ss3654008762, ss3825454863, ss3986866476, ss5441587618, ss5512474023, ss5848570320 NC_000022.10:42525088:G:C NC_000022.11:42129086:G:C (self)
106410758, 571270030, 385889689, 9486241505, ss5110780742, ss5311255667, ss5503082687, ss5618884823 NC_000022.11:42129086:G:C NC_000022.11:42129086:G:C (self)
ss141047260, ss159831293 NT_011520.12:21915657:G:C NC_000022.11:42129086:G:C (self)
Help

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

1 citation for rs78482768
PMID Title Author Year Journal
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
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.post825+45319f0