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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.

rs72549347

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr22:42127590 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000159 (40/250980, GnomAD_exome)
A=0.000522 (73/139764, GnomAD)
A=0.000191 (23/120558, ExAC) (+ 6 more)
A=0.00024 (8/33230, ALFA)
A=0.00004 (1/28202, 14KJPN)
A=0.00006 (1/16726, 8.3KJPN)
A=0.00077 (10/13000, GO-ESP)
A=0.0002 (1/6404, 1000G_30x)
A=0.0002 (1/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CYP2D6 : Stop Gained
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 49568 G=0.99954 A=0.00046 0.999072 0.0 0.000928 0
European Sub 34592 G=0.99994 A=0.00006 0.999884 0.0 0.000116 0
African Sub 7658 G=0.9973 A=0.0027 0.994516 0.0 0.005484 0
African Others Sub 290 G=0.990 A=0.010 0.97931 0.0 0.02069 0
African American Sub 7368 G=0.9976 A=0.0024 0.995114 0.0 0.004886 0
Asian Sub 108 G=1.000 A=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 500 G=1.000 A=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 628 G=1.000 A=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 G=1.00 A=0.00 1.0 0.0 0.0 N/A
Other Sub 5988 G=1.0000 A=0.0000 1.0 0.0 0.0 N/A


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
gnomAD - Exomes Global Study-wide 250980 G=0.999841 A=0.000159
gnomAD - Exomes European Sub 135128 G=0.999963 A=0.000037
gnomAD - Exomes Asian Sub 48912 G=0.99994 A=0.00006
gnomAD - Exomes American Sub 34548 G=0.99980 A=0.00020
gnomAD - Exomes African Sub 16184 G=0.99846 A=0.00154
gnomAD - Exomes Ashkenazi Jewish Sub 10080 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6128 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 139764 G=0.999478 A=0.000522
gnomAD - Genomes European Sub 75790 G=0.99997 A=0.00003
gnomAD - Genomes African Sub 41758 G=0.99837 A=0.00163
gnomAD - Genomes American Sub 13620 G=0.99993 A=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3128 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2144 G=0.9991 A=0.0009
ExAC Global Study-wide 120558 G=0.999809 A=0.000191
ExAC Europe Sub 72890 G=0.99995 A=0.00005
ExAC Asian Sub 25004 G=0.99996 A=0.00004
ExAC American Sub 11496 G=0.99991 A=0.00009
ExAC African Sub 10262 G=0.99834 A=0.00166
ExAC Other Sub 906 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 33230 G=0.99976 A=0.00024
Allele Frequency Aggregator European Sub 24510 G=0.99992 A=0.00008
Allele Frequency Aggregator Other Sub 4554 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2836 G=0.9979 A=0.0021
Allele Frequency Aggregator Latin American 2 Sub 628 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 108 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 94 G=1.00 A=0.00
14KJPN JAPANESE Study-wide 28202 G=0.99996 A=0.00004
8.3KJPN JAPANESE Study-wide 16726 G=0.99994 A=0.00006
GO Exome Sequencing Project Global Study-wide 13000 G=0.99923 A=0.00077
GO Exome Sequencing Project European American Sub 8596 G=0.9999 A=0.0001
GO Exome Sequencing Project African American Sub 4404 G=0.9980 A=0.0020
1000Genomes_30x Global Study-wide 6404 G=0.9998 A=0.0002
1000Genomes_30x African Sub 1786 G=0.9994 A=0.0006
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9998 A=0.0002
1000Genomes African Sub 1322 G=0.9992 A=0.0008
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
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.42127590G>A
gene/pseudogene RefSeqGene (LRG_303) NG_008376.4:g.8221C>T
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1 NW_015148968.1:g.5331G>A
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1 NW_014040931.1:g.21179G>A
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1 NW_009646208.1:g.13156G>A
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1 NW_004504305.1:g.49917G>A
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1 NT_187682.1:g.49931G>A
GRCh37.p13 chr 22 NC_000022.10:g.42523592G>A
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.1030C>T R [CGA] > * [TGA] Coding Sequence Variant
cytochrome P450 2D6 isoform 1 NP_000097.3:p.Arg344Ter R (Arg) > * (Ter) Stop Gained
CYP2D6 transcript variant 2 NM_001025161.3:c.877C>T R [CGA] > * [TGA] Coding Sequence Variant
cytochrome P450 2D6 isoform 2 NP_001020332.2:p.Arg293Ter R (Arg) > * (Ter) Stop Gained
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
GRCh38.p14 chr 22 NC_000022.11:g.42127590= NC_000022.11:g.42127590G>A
gene/pseudogene RefSeqGene (LRG_303) NG_008376.4:g.8221= NG_008376.4:g.8221C>T
CYP2D6 transcript variant 1 NM_000106.6:c.1030= NM_000106.6:c.1030C>T
CYP2D6 transcript variant 1 NM_000106.5:c.1030= NM_000106.5:c.1030C>T
CYP2D6 transcript variant 2 NM_001025161.3:c.877= NM_001025161.3:c.877C>T
CYP2D6 transcript variant 2 NM_001025161.2:c.877= NM_001025161.2:c.877C>T
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1 NW_015148968.1:g.5331= NW_015148968.1:g.5331G>A
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1 NW_014040931.1:g.21179= NW_014040931.1:g.21179G>A
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1 NW_009646208.1:g.13156= NW_009646208.1:g.13156G>A
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1 NW_004504305.1:g.49917= NW_004504305.1:g.49917G>A
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1 NT_187682.1:g.49931= NT_187682.1:g.49931G>A
GRCh37.p13 chr 22 NC_000022.10:g.42523592= NC_000022.10:g.42523592G>A
cytochrome P450 2D6 isoform 1 NP_000097.3:p.Arg344= NP_000097.3:p.Arg344Ter
cytochrome P450 2D6 isoform 2 NP_001020332.2:p.Arg293= NP_001020332.2:p.Arg293Ter
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#.

15 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 AFFY_DM3_1 ss105434364 Feb 13, 2009 (130)
2 NHLBI-ESP ss342544603 May 09, 2011 (147)
3 1000GENOMES ss1367336040 Aug 21, 2014 (147)
4 EVA_EXAC ss1694379049 Apr 01, 2015 (147)
5 GNOMAD ss2745191387 Nov 08, 2017 (151)
6 GNOMAD ss2750571559 Nov 08, 2017 (151)
7 GNOMAD ss2974893411 Nov 08, 2017 (151)
8 EVA ss3825454779 Apr 27, 2020 (154)
9 TOMMO_GENOMICS ss5232837035 Apr 26, 2021 (155)
10 EVA ss5441587462 Oct 16, 2022 (156)
11 EVA ss5512473995 Oct 16, 2022 (156)
12 1000G_HIGH_COVERAGE ss5618884682 Oct 16, 2022 (156)
13 TOMMO_GENOMICS ss5794028991 Oct 16, 2022 (156)
14 EVA ss5936464374 Oct 16, 2022 (156)
15 EVA ss5979638951 Oct 16, 2022 (156)
16 1000Genomes NC_000022.10 - 42523592 Oct 12, 2018 (152)
17 1000Genomes_30x NC_000022.11 - 42127590 Oct 16, 2022 (156)
18 ExAC NC_000022.10 - 42523592 Oct 12, 2018 (152)
19 gnomAD - Genomes NC_000022.11 - 42127590 Apr 26, 2021 (155)
20 gnomAD - Exomes NC_000022.10 - 42523592 Jul 13, 2019 (153)
21 GO Exome Sequencing Project NC_000022.10 - 42523592 Oct 12, 2018 (152)
22 8.3KJPN NC_000022.10 - 42523592 Apr 26, 2021 (155)
23 14KJPN NC_000022.11 - 42127590 Oct 16, 2022 (156)
24 ALFA NC_000022.11 - 42127590 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).

Associated ID History Updated (Build)
rs147960066 Jul 19, 2016 (147)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
80894455, 5962333, 14524103, 1911609, 90806342, ss342544603, ss1367336040, ss1694379049, ss2745191387, ss2750571559, ss2974893411, ss3825454779, ss5232837035, ss5441587462, ss5512473995, ss5936464374, ss5979638951 NC_000022.10:42523591:G:A NC_000022.11:42127589:G:A (self)
106410617, 571269424, 127866095, 8320346779, ss5618884682, ss5794028991 NC_000022.11:42127589:G:A NC_000022.11:42127589:G:A (self)
ss105434364 NT_011520.12:21914160:G:A NC_000022.11:42127589:G:A (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 rs72549347
PMID Title Author Year Journal
34621706 Comprehensive analysis of important pharmacogenes in Koreans using the DMET™ platform. Kim B et al. 2021 Translational and 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.post825+45319f0