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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.

rs72549358

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr22:42130773 (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>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.002728 (722/264690, TOPMED)
T=0.002421 (482/199058, GnomAD_exome)
T=0.002498 (348/139284, GnomAD) (+ 9 more)
T=0.00303 (218/71948, ALFA)
T=0.00328 (144/43902, ExAC)
T=0.00255 (33/12958, GO-ESP)
T=0.0011 (7/6404, 1000G_30x)
T=0.0012 (6/5008, 1000G)
T=0.0057 (22/3854, ALSPAC)
T=0.0035 (13/3708, TWINSUK)
T=0.003 (3/998, GoNL)
T=0.009 (5/534, MGP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CYP2D6 : Missense Variant
LOC102723722 : Intron 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 88270 C=0.99707 T=0.00293 0.994245 0.000113 0.005642 30
European Sub 69492 C=0.99682 T=0.00318 0.993783 0.000144 0.006073 33
African Sub 8378 C=0.9994 T=0.0006 0.998806 0.0 0.001194 0
African Others Sub 304 C=1.000 T=0.000 1.0 0.0 0.0 N/A
African American Sub 8074 C=0.9994 T=0.0006 0.998761 0.0 0.001239 0
Asian Sub 212 C=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 156 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=0.990 T=0.010 0.98 0.0 0.02 0
Latin American 2 Sub 628 C=0.997 T=0.003 0.993631 0.0 0.006369 0
South Asian Sub 98 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 8962 C=0.9971 T=0.0029 0.994198 0.0 0.005802 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 C=0.997272 T=0.002728
gnomAD - Exomes Global Study-wide 199058 C=0.997579 T=0.002421
gnomAD - Exomes European Sub 102234 C=0.997183 T=0.002817
gnomAD - Exomes Asian Sub 41634 C=0.99971 T=0.00029
gnomAD - Exomes American Sub 29216 C=0.99456 T=0.00544
gnomAD - Exomes African Sub 11732 C=0.99932 T=0.00068
gnomAD - Exomes Ashkenazi Jewish Sub 9124 C=0.9998 T=0.0002
gnomAD - Exomes Other Sub 5118 C=0.9975 T=0.0025
gnomAD - Genomes Global Study-wide 139284 C=0.997502 T=0.002498
gnomAD - Genomes European Sub 75682 C=0.99695 T=0.00305
gnomAD - Genomes African Sub 41436 C=0.99930 T=0.00070
gnomAD - Genomes American Sub 13592 C=0.99485 T=0.00515
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.9985 T=0.0015
gnomAD - Genomes East Asian Sub 3114 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2138 C=0.9939 T=0.0061
Allele Frequency Aggregator Total Global 71948 C=0.99697 T=0.00303
Allele Frequency Aggregator European Sub 59422 C=0.99684 T=0.00316
Allele Frequency Aggregator Other Sub 7528 C=0.9971 T=0.0029
Allele Frequency Aggregator African Sub 3560 C=0.9997 T=0.0003
Allele Frequency Aggregator Latin American 2 Sub 628 C=0.997 T=0.003
Allele Frequency Aggregator Latin American 1 Sub 500 C=0.990 T=0.010
Allele Frequency Aggregator Asian Sub 212 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
ExAC Global Study-wide 43902 C=0.99672 T=0.00328
ExAC Europe Sub 23248 C=0.99544 T=0.00456
ExAC Asian Sub 13248 C=0.99955 T=0.00045
ExAC African Sub 4346 C=0.9988 T=0.0012
ExAC American Sub 2712 C=0.9908 T=0.0092
ExAC Other Sub 348 C=0.994 T=0.006
GO Exome Sequencing Project Global Study-wide 12958 C=0.99745 T=0.00255
GO Exome Sequencing Project European American Sub 8576 C=0.9969 T=0.0031
GO Exome Sequencing Project African American Sub 4382 C=0.9986 T=0.0014
1000Genomes_30x Global Study-wide 6404 C=0.9989 T=0.0011
1000Genomes_30x African Sub 1786 C=1.0000 T=0.0000
1000Genomes_30x Europe Sub 1266 C=0.9953 T=0.0047
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=0.9988 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=0.9950 T=0.0050
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=0.9943 T=0.0057
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9965 T=0.0035
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.997 T=0.003
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.991 T=0.009
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.42130773C>A
GRCh38.p14 chr 22 NC_000022.11:g.42130773C>G
GRCh38.p14 chr 22 NC_000022.11:g.42130773C>T
gene/pseudogene RefSeqGene (LRG_303) NG_008376.4:g.5038G>T
gene/pseudogene RefSeqGene (LRG_303) NG_008376.4:g.5038G>C
gene/pseudogene RefSeqGene (LRG_303) NG_008376.4:g.5038G>A
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1 NW_015148968.1:g.8514C>A
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1 NW_015148968.1:g.8514C>G
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1 NW_015148968.1:g.8514C>T
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1 NW_014040931.1:g.24362C>A
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1 NW_014040931.1:g.24362C>G
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1 NW_014040931.1:g.24362C>T
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1 NW_009646208.1:g.16339C>A
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1 NW_009646208.1:g.16339C>G
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1 NW_009646208.1:g.16339C>T
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1 NW_004504305.1:g.53100C>A
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1 NW_004504305.1:g.53100C>G
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1 NW_004504305.1:g.53100C>T
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1 NT_187682.1:g.53114C>A
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1 NT_187682.1:g.53114C>G
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1 NT_187682.1:g.53114C>T
GRCh37.p13 chr 22 NC_000022.10:g.42526775C>A
GRCh37.p13 chr 22 NC_000022.10:g.42526775C>G
GRCh37.p13 chr 22 NC_000022.10:g.42526775C>T
LOC110740340 genomic region NG_055460.1:g.58C>A
LOC110740340 genomic region NG_055460.1:g.58C>G
LOC110740340 genomic region NG_055460.1:g.58C>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.19G>T V [GTG] > L [TTG] Coding Sequence Variant
cytochrome P450 2D6 isoform 1 NP_000097.3:p.Val7Leu V (Val) > L (Leu) Missense Variant
CYP2D6 transcript variant 1 NM_000106.6:c.19G>C V [GTG] > L [CTG] Coding Sequence Variant
cytochrome P450 2D6 isoform 1 NP_000097.3:p.Val7Leu V (Val) > L (Leu) Missense Variant
CYP2D6 transcript variant 1 NM_000106.6:c.19G>A V [GTG] > M [ATG] Coding Sequence Variant
cytochrome P450 2D6 isoform 1 NP_000097.3:p.Val7Met V (Val) > M (Met) Missense Variant
CYP2D6 transcript variant 2 NM_001025161.3:c.19G>T V [GTG] > L [TTG] Coding Sequence Variant
cytochrome P450 2D6 isoform 2 NP_001020332.2:p.Val7Leu V (Val) > L (Leu) Missense Variant
CYP2D6 transcript variant 2 NM_001025161.3:c.19G>C V [GTG] > L [CTG] Coding Sequence Variant
cytochrome P450 2D6 isoform 2 NP_001020332.2:p.Val7Leu V (Val) > L (Leu) Missense Variant
CYP2D6 transcript variant 2 NM_001025161.3:c.19G>A V [GTG] > M [ATG] Coding Sequence Variant
cytochrome P450 2D6 isoform 2 NP_001020332.2:p.Val7Met V (Val) > M (Met) 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 C= A G T
GRCh38.p14 chr 22 NC_000022.11:g.42130773= NC_000022.11:g.42130773C>A NC_000022.11:g.42130773C>G NC_000022.11:g.42130773C>T
gene/pseudogene RefSeqGene (LRG_303) NG_008376.4:g.5038= NG_008376.4:g.5038G>T NG_008376.4:g.5038G>C NG_008376.4:g.5038G>A
CYP2D6 transcript variant 1 NM_000106.6:c.19= NM_000106.6:c.19G>T NM_000106.6:c.19G>C NM_000106.6:c.19G>A
CYP2D6 transcript variant 1 NM_000106.5:c.19= NM_000106.5:c.19G>T NM_000106.5:c.19G>C NM_000106.5:c.19G>A
CYP2D6 transcript variant 2 NM_001025161.3:c.19= NM_001025161.3:c.19G>T NM_001025161.3:c.19G>C NM_001025161.3:c.19G>A
CYP2D6 transcript variant 2 NM_001025161.2:c.19= NM_001025161.2:c.19G>T NM_001025161.2:c.19G>C NM_001025161.2:c.19G>A
GRCh38.p14 chr 22 novel patch HSCHR22_8_CTG1 NW_015148968.1:g.8514= NW_015148968.1:g.8514C>A NW_015148968.1:g.8514C>G NW_015148968.1:g.8514C>T
GRCh38.p14 chr 22 novel patch HSCHR22_7_CTG1 NW_014040931.1:g.24362= NW_014040931.1:g.24362C>A NW_014040931.1:g.24362C>G NW_014040931.1:g.24362C>T
GRCh38.p14 chr 22 novel patch HSCHR22_5_CTG1 NW_009646208.1:g.16339= NW_009646208.1:g.16339C>A NW_009646208.1:g.16339C>G NW_009646208.1:g.16339C>T
GRCh38.p14 chr 22 alt locus HSCHR22_2_CTG1 NW_004504305.1:g.53100= NW_004504305.1:g.53100C>A NW_004504305.1:g.53100C>G NW_004504305.1:g.53100C>T
GRCh38.p14 chr 22 alt locus HSCHR22_3_CTG1 NT_187682.1:g.53114= NT_187682.1:g.53114C>A NT_187682.1:g.53114C>G NT_187682.1:g.53114C>T
GRCh37.p13 chr 22 NC_000022.10:g.42526775= NC_000022.10:g.42526775C>A NC_000022.10:g.42526775C>G NC_000022.10:g.42526775C>T
LOC110740340 genomic region NG_055460.1:g.58= NG_055460.1:g.58C>A NG_055460.1:g.58C>G NG_055460.1:g.58C>T
cytochrome P450 2D6 isoform 1 NP_000097.3:p.Val7= NP_000097.3:p.Val7Leu NP_000097.3:p.Val7Leu NP_000097.3:p.Val7Met
cytochrome P450 2D6 isoform 2 NP_001020332.2:p.Val7= NP_001020332.2:p.Val7Leu NP_001020332.2:p.Val7Leu NP_001020332.2:p.Val7Met
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#.

35 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 AFFY_DM3_1 ss105434379 Feb 13, 2009 (130)
2 EGP_SNPS ss159831265 Dec 01, 2009 (131)
3 BL ss255929820 May 09, 2011 (134)
4 NHLBI-ESP ss342544657 May 09, 2011 (134)
5 EXOME_CHIP ss491572639 May 04, 2012 (137)
6 EVA-GONL ss995393830 Aug 21, 2014 (142)
7 1000GENOMES ss1367336251 Aug 21, 2014 (142)
8 EVA_UK10K_ALSPAC ss1640083689 Apr 01, 2015 (144)
9 EVA_UK10K_TWINSUK ss1683077722 Apr 01, 2015 (144)
10 EVA_EXAC ss1694379715 Apr 01, 2015 (144)
11 EVA_DECODE ss1699465093 Apr 01, 2015 (144)
12 EVA_MGP ss1711571606 Apr 01, 2015 (144)
13 JJLAB ss2030253512 Sep 14, 2016 (149)
14 ILLUMINA ss2710959504 Nov 08, 2017 (151)
15 GNOMAD ss2745192305 Nov 08, 2017 (151)
16 GNOMAD ss2750571896 Nov 08, 2017 (151)
17 GNOMAD ss2974893970 Nov 08, 2017 (151)
18 AFFY ss2985240519 Nov 08, 2017 (151)
19 AFFY ss2985857688 Nov 08, 2017 (151)
20 SWEGEN ss3019375590 Nov 08, 2017 (151)
21 ILLUMINA ss3654008774 Oct 12, 2018 (152)
22 EVA_DECODE ss3708287400 Jul 13, 2019 (153)
23 EVA ss3825454921 Apr 27, 2020 (154)
24 EVA ss3825972724 Apr 27, 2020 (154)
25 EVA ss3986866524 Apr 26, 2021 (155)
26 TOPMED ss5110781433 Apr 26, 2021 (155)
27 1000G_HIGH_COVERAGE ss5311255752 Oct 16, 2022 (156)
28 EVA ss5441587782 Oct 16, 2022 (156)
29 HUGCELL_USP ss5503082749 Oct 16, 2022 (156)
30 EVA ss5512474053 Oct 16, 2022 (156)
31 1000G_HIGH_COVERAGE ss5618884952 Oct 16, 2022 (156)
32 EVA ss5822131273 Oct 16, 2022 (156)
33 EVA ss5848570349 Oct 16, 2022 (156)
34 EVA ss5936465300 Oct 16, 2022 (156)
35 EVA ss5959434953 Oct 16, 2022 (156)
36 1000Genomes NC_000022.10 - 42526775 Oct 12, 2018 (152)
37 1000Genomes_30x NC_000022.11 - 42130773 Oct 16, 2022 (156)
38 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 42526775 Oct 12, 2018 (152)
39 ExAC NC_000022.10 - 42526775 Oct 12, 2018 (152)
40 gnomAD - Genomes NC_000022.11 - 42130773 Apr 26, 2021 (155)
41 gnomAD - Exomes NC_000022.10 - 42526775 Jul 13, 2019 (153)
42 GO Exome Sequencing Project NC_000022.10 - 42526775 Oct 12, 2018 (152)
43 Genome of the Netherlands Release 5 NC_000022.10 - 42526775 Apr 27, 2020 (154)
44 Medical Genome Project healthy controls from Spanish population NC_000022.10 - 42526775 Apr 27, 2020 (154)
45 TopMed NC_000022.11 - 42130773 Apr 26, 2021 (155)
46 UK 10K study - Twins NC_000022.10 - 42526775 Oct 12, 2018 (152)
47 ALFA NC_000022.11 - 42130773 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
ss5512474053, ss5936465300 NC_000022.10:42526774:C:A NC_000022.11:42130772:C:A
ss5936465300 NC_000022.10:42526774:C:G NC_000022.11:42130772:C:G
ss255929820, ss1699465093 NC_000022.9:40856718:C:T NC_000022.11:42130772:C:T (self)
80894673, 44747546, 5963048, 14525097, 1911749, 19935881, 687366, 44747546, ss342544657, ss491572639, ss995393830, ss1367336251, ss1640083689, ss1683077722, ss1694379715, ss1711571606, ss2030253512, ss2710959504, ss2745192305, ss2750571896, ss2974893970, ss2985240519, ss2985857688, ss3019375590, ss3654008774, ss3825454921, ss3825972724, ss3986866524, ss5441587782, ss5512474053, ss5822131273, ss5848570349, ss5959434953 NC_000022.10:42526774:C:T NC_000022.11:42130772:C:T (self)
106410887, 571270614, 385890380, 374385348, ss3708287400, ss5110781433, ss5311255752, ss5503082749, ss5618884952 NC_000022.11:42130772:C:T NC_000022.11:42130772:C:T (self)
ss105434379, ss159831265 NT_011520.12:21917343:C:T NC_000022.11:42130772: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.

1 citation for rs72549358
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