Name: rs79292917
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.

rs79292917

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:42127852 (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=0.002225 (589/264690, TOPMED)
T=0.002869 (720/250956, GnomAD_exome)
T=0.002670 (372/139326, GnomAD) (+ 14 more)
T=0.003337 (403/120752, ExAC)
T=0.00428 (211/49288, ALFA)
T=0.00004 (1/28170, 14KJPN)
T=0.00262 (34/12988, GO-ESP)
T=0.0006 (4/6404, 1000G_30x)
T=0.0006 (3/5008, 1000G)
T=0.0036 (14/3854, ALSPAC)
T=0.0032 (12/3708, TWINSUK)
T=0.0000 (0/2918, KOREAN)
T=0.003 (3/998, GoNL)
T=0.020 (12/600, NorthernSweden)
T=0.010 (3/304, FINRISK)
C=0.5 (1/2, Siberian)
T=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CYP2D6 : Synonymous Variant
Publications: 0 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	49288	C=0.99572	T=0.00428	0.991844	0.000406	0.00775	32
European	Sub	37266	C=0.99541	T=0.00459	0.991252	0.000429	0.008319	32
African	Sub	3572	C=0.9980	T=0.0020	0.996641	0.00056	0.0028	32
African Others	Sub	122	C=1.000	T=0.000	1.0	0.0	0.0	N/A
African American	Sub	3450	C=0.9980	T=0.0020	0.996522	0.00058	0.002899	32
Asian	Sub	168	C=1.000	T=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	112	C=1.000	T=0.000	1.0	0.0	0.0	N/A
Other Asian	Sub	56	C=1.00	T=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	500	C=0.998	T=0.002	0.996	0.0	0.004	0
Latin American 2	Sub	628	C=1.000	T=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	98	C=1.00	T=0.00	1.0	0.0	0.0	N/A
Other	Sub	7056	C=0.9955	T=0.0045	0.991213	0.000283	0.008503	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=0.997775	T=0.002225
gnomAD - Exomes	Global	Study-wide	250956	C=0.997131	T=0.002869
gnomAD - Exomes	European	Sub	135106	C=0.995315	T=0.004685
gnomAD - Exomes	Asian	Sub	48906	C=0.99994	T=0.00006
gnomAD - Exomes	American	Sub	34546	C=0.99928	T=0.00072
gnomAD - Exomes	African	Sub	16192	C=0.99907	T=0.00093
gnomAD - Exomes	Ashkenazi Jewish	Sub	10076	C=0.99752	T=0.00248
gnomAD - Exomes	Other	Sub	6130	C=0.9969	T=0.0031
gnomAD - Genomes	Global	Study-wide	139326	C=0.997330	T=0.002670
gnomAD - Genomes	European	Sub	75642	C=0.99590	T=0.00410
gnomAD - Genomes	African	Sub	41514	C=0.99904	T=0.00096
gnomAD - Genomes	American	Sub	13580	C=0.99897	T=0.00103
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9988	T=0.0012
gnomAD - Genomes	East Asian	Sub	3122	C=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2144	C=0.9981	T=0.0019
ExAC	Global	Study-wide	120752	C=0.996663	T=0.003337
ExAC	Europe	Sub	72940	C=0.99471	T=0.00529
ExAC	Asian	Sub	25082	C=0.99996	T=0.00004
ExAC	American	Sub	11560	C=0.99931	T=0.00069
ExAC	African	Sub	10262	C=0.99922	T=0.00078
ExAC	Other	Sub	908	C=1.000	T=0.000
Allele Frequency Aggregator	Total	Global	49288	C=0.99572	T=0.00428
Allele Frequency Aggregator	European	Sub	37266	C=0.99541	T=0.00459
Allele Frequency Aggregator	Other	Sub	7056	C=0.9955	T=0.0045
Allele Frequency Aggregator	African	Sub	3572	C=0.9980	T=0.0020
Allele Frequency Aggregator	Latin American 2	Sub	628	C=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	500	C=0.998	T=0.002
Allele Frequency Aggregator	Asian	Sub	168	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	T=0.00
14KJPN	JAPANESE	Study-wide	28170	C=0.99996	T=0.00004
GO Exome Sequencing Project	Global	Study-wide	12988	C=0.99738	T=0.00262
GO Exome Sequencing Project	European American	Sub	8596	C=0.9967	T=0.0033
GO Exome Sequencing Project	African American	Sub	4392	C=0.9986	T=0.0014
1000Genomes_30x	Global	Study-wide	6404	C=0.9994	T=0.0006
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=0.999	T=0.001
1000Genomes	Global	Study-wide	5008	C=0.9994	T=0.0006
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=0.999	T=0.001
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9964	T=0.0036
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9968	T=0.0032
KOREAN population from KRGDB	KOREAN	Study-wide	2918	C=1.0000	T=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.997	T=0.003
Northern Sweden	ACPOP	Study-wide	600	C=0.980	T=0.020
FINRISK	Finnish from FINRISK project	Study-wide	304	C=0.990	T=0.010
Siberian	Global	Study-wide	2	C=0.5	T=0.5

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.42127852C>T
gene/pseudogene RefSeqGene (LRG_303)	NG_008376.4:g.7959G>A
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1	NW_015148968.1:g.5593C>T
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1	NW_014040931.1:g.21441C>T
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1	NW_009646208.1:g.13418C>T
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1	NW_004504305.1:g.50179C>T
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1	NT_187682.1:g.50193C>T
GRCh37.p13 chr 22	NC_000022.10:g.42523854C>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.975G>A	P [CCG] > P [CCA]	Coding Sequence Variant
cytochrome P450 2D6 isoform 1	NP_000097.3:p.Pro325=	P (Pro) > P (Pro)	Synonymous Variant
CYP2D6 transcript variant 2	NM_001025161.3:c.822G>A	P [CCG] > P [CCA]	Coding Sequence Variant
cytochrome P450 2D6 isoform 2	NP_001020332.2:p.Pro274=	P (Pro) > P (Pro)	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=	T
GRCh38.p14 chr 22	NC_000022.11:g.42127852=	NC_000022.11:g.42127852C>T
gene/pseudogene RefSeqGene (LRG_303)	NG_008376.4:g.7959=	NG_008376.4:g.7959G>A
CYP2D6 transcript variant 1	NM_000106.6:c.975=	NM_000106.6:c.975G>A
CYP2D6 transcript variant 1	NM_000106.5:c.975=	NM_000106.5:c.975G>A
CYP2D6 transcript variant 2	NM_001025161.3:c.822=	NM_001025161.3:c.822G>A
CYP2D6 transcript variant 2	NM_001025161.2:c.822=	NM_001025161.2:c.822G>A
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1	NW_015148968.1:g.5593=	NW_015148968.1:g.5593C>T
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1	NW_014040931.1:g.21441=	NW_014040931.1:g.21441C>T
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1	NW_009646208.1:g.13418=	NW_009646208.1:g.13418C>T
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1	NW_004504305.1:g.50179=	NW_004504305.1:g.50179C>T
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1	NT_187682.1:g.50193=	NT_187682.1:g.50193C>T
GRCh37.p13 chr 22	NC_000022.10:g.42523854=	NC_000022.10:g.42523854C>T
cytochrome P450 2D6 isoform 1	NP_000097.3:p.Pro325=	NP_000097.3:p.Pro325=
cytochrome P450 2D6 isoform 2	NP_001020332.2:p.Pro274=	NP_001020332.2:p.Pro274=

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#.

36 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	RWHITE	ss141047244	Dec 01, 2009 (131)
2	NHLBI-ESP	ss342544609	May 09, 2011 (134)
3	1000GENOMES	ss489219213	May 04, 2012 (137)
4	CLINSEQ_SNP	ss491825724	May 04, 2012 (137)
5	EVA-GONL	ss995393790	Aug 21, 2014 (142)
6	1000GENOMES	ss1367336061	Aug 21, 2014 (142)
7	EVA_FINRISK	ss1584128341	Apr 01, 2015 (144)
8	EVA_UK10K_ALSPAC	ss1640083669	Apr 01, 2015 (144)
9	EVA_UK10K_TWINSUK	ss1683077702	Apr 01, 2015 (144)
10	EVA_EXAC	ss1694379124	Apr 01, 2015 (144)
11	EVA_DECODE	ss1699465063	Apr 01, 2015 (144)
12	USC_VALOUEV	ss2158873703	Dec 20, 2016 (150)
13	GNOMAD	ss2745191475	Nov 08, 2017 (151)
14	GNOMAD	ss2750571597	Nov 08, 2017 (151)
15	GNOMAD	ss2974893464	Nov 08, 2017 (151)
16	SWEGEN	ss3019375490	Nov 08, 2017 (151)
17	EVA_DECODE	ss3708287341	Jul 13, 2019 (153)
18	ACPOP	ss3743969259	Jul 13, 2019 (153)
19	EVA	ss3825454798	Apr 27, 2020 (154)
20	EVA	ss3825972709	Apr 27, 2020 (154)
21	KRGDB	ss3941034956	Apr 27, 2020 (154)
22	TOPMED	ss5110780144	Apr 26, 2021 (155)
23	EVA	ss5237676611	Oct 16, 2022 (156)
24	1000G_HIGH_COVERAGE	ss5311255578	Oct 16, 2022 (156)
25	EVA	ss5441587490	Oct 16, 2022 (156)
26	HUGCELL_USP	ss5503082644	Oct 16, 2022 (156)
27	EVA	ss5512473998	Oct 16, 2022 (156)
28	1000G_HIGH_COVERAGE	ss5618884705	Oct 16, 2022 (156)
29	TOMMO_GENOMICS	ss5794029021	Oct 16, 2022 (156)
30	EVA	ss5822131211	Oct 16, 2022 (156)
31	EVA	ss5847519178	Oct 16, 2022 (156)
32	EVA	ss5847946430	Oct 16, 2022 (156)
33	EVA	ss5848570299	Oct 16, 2022 (156)
34	EVA	ss5936464520	Oct 16, 2022 (156)
35	EVA	ss5959434893	Oct 16, 2022 (156)
36	EVA	ss5979638955	Oct 16, 2022 (156)
37	1000Genomes	NC_000022.10 - 42523854	Oct 12, 2018 (152)
38	1000Genomes_30x	NC_000022.11 - 42127852	Oct 16, 2022 (156)
39	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 42523854	Oct 12, 2018 (152)
40	ExAC	NC_000022.10 - 42523854	Oct 12, 2018 (152)
41	FINRISK	NC_000022.10 - 42523854	Apr 27, 2020 (154)
42	gnomAD - Genomes	NC_000022.11 - 42127852	Apr 26, 2021 (155)
43	gnomAD - Exomes	NC_000022.10 - 42523854	Jul 13, 2019 (153)
44	GO Exome Sequencing Project	NC_000022.10 - 42523854	Oct 12, 2018 (152)
45	Genome of the Netherlands Release 5	NC_000022.10 - 42523854	Apr 27, 2020 (154)
46	KOREAN population from KRGDB	NC_000022.10 - 42523854	Apr 27, 2020 (154)
47	Northern Sweden	NC_000022.10 - 42523854	Jul 13, 2019 (153)
48	Siberian	NC_000022.10 - 42523854	Apr 27, 2020 (154)
49	14KJPN	NC_000022.11 - 42127852	Oct 16, 2022 (156)
50	TopMed	NC_000022.11 - 42127852	Apr 26, 2021 (155)
51	UK 10K study - Twins	NC_000022.10 - 42523854	Oct 12, 2018 (152)
52	ALFA	NC_000022.11 - 42127852	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss491825724, ss1699465063	NC_000022.9:40853797:C:T	NC_000022.11:42127851:C:T	(self)
80894477, 44747521, 5962413, 124802, 14524204, 1911628, 19935854, 48212350, 17254124, 11390057, 44747521, ss342544609, ss489219213, ss995393790, ss1367336061, ss1584128341, ss1640083669, ss1683077702, ss1694379124, ss2158873703, ss2745191475, ss2750571597, ss2974893464, ss3019375490, ss3743969259, ss3825454798, ss3825972709, ss3941034956, ss5441587490, ss5512473998, ss5822131211, ss5847519178, ss5847946430, ss5848570299, ss5936464520, ss5959434893, ss5979638955	NC_000022.10:42523853:C:T	NC_000022.11:42127851:C:T	(self)
106410640, 571269540, 127866125, 385889091, 12021498163, ss3708287341, ss5110780144, ss5237676611, ss5311255578, ss5503082644, ss5618884705, ss5794029021	NC_000022.11:42127851:C:T	NC_000022.11:42127851:C:T	(self)
ss141047244	NT_011520.12:21914422:C:T	NC_000022.11:42127851:C:T	(self)

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

No publications for rs79292917

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

rs79292917