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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.

rs5993882

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr22:19950010 (GRCh38.p13) 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
T>C / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.264400 (69984/264690, TOPMED)
G=0.255501 (35761/139964, GnomAD)
G=0.14660 (2998/20450, ALFA) (+ 17 more)
G=0.11963 (2005/16760, 8.3KJPN)
G=0.2496 (1250/5008, 1000G)
G=0.1949 (873/4480, Estonian)
G=0.2224 (857/3854, ALSPAC)
G=0.2400 (890/3708, TWINSUK)
G=0.1057 (309/2922, KOREAN)
G=0.2739 (516/1884, HapMap)
G=0.243 (243/998, GoNL)
G=0.083 (63/756, PRJEB37584)
G=0.264 (165/626, Chileans)
G=0.223 (134/600, NorthernSweden)
G=0.208 (45/216, Qatari)
G=0.099 (21/212, Vietnamese)
T=0.444 (88/198, SGDP_PRJ)
G=0.25 (10/40, GENOME_DK)
T=0.50 (10/20, Siberian)
G=0.50 (10/20, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
COMT : Intron Variant
Publications
12 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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 20450 T=0.85340 C=0.00000, G=0.14660
European Sub 14250 T=0.85572 C=0.00000, G=0.14428
African Sub 2054 T=0.8690 C=0.0000, G=0.1310
African Others Sub 70 T=0.91 C=0.00, G=0.09
African American Sub 1984 T=0.8674 C=0.0000, G=0.1326
Asian Sub 134 T=0.963 C=0.000, G=0.037
East Asian Sub 80 T=0.97 C=0.00, G=0.03
Other Asian Sub 54 T=0.94 C=0.00, G=0.06
Latin American 1 Sub 230 T=0.817 C=0.000, G=0.183
Latin American 2 Sub 2566 T=0.8352 C=0.0000, G=0.1648
South Asian Sub 80 T=0.95 C=0.00, G=0.05
Other Sub 1136 T=0.8248 C=0.0000, G=0.1752


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 T=0.735600 G=0.264400
gnomAD - Genomes Global Study-wide 139964 T=0.744499 G=0.255501
gnomAD - Genomes European Sub 75840 T=0.77608 G=0.22392
gnomAD - Genomes African Sub 41914 T=0.67345 G=0.32655
gnomAD - Genomes American Sub 13614 T=0.75283 G=0.24717
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=0.7578 G=0.2422
gnomAD - Genomes East Asian Sub 3128 T=0.8878 G=0.1122
gnomAD - Genomes Other Sub 2148 T=0.7337 G=0.2663
Allele Frequency Aggregator Total Global 20450 T=0.85340 C=0.00000, G=0.14660
Allele Frequency Aggregator European Sub 14250 T=0.85572 C=0.00000, G=0.14428
Allele Frequency Aggregator Latin American 2 Sub 2566 T=0.8352 C=0.0000, G=0.1648
Allele Frequency Aggregator African Sub 2054 T=0.8690 C=0.0000, G=0.1310
Allele Frequency Aggregator Other Sub 1136 T=0.8248 C=0.0000, G=0.1752
Allele Frequency Aggregator Latin American 1 Sub 230 T=0.817 C=0.000, G=0.183
Allele Frequency Aggregator Asian Sub 134 T=0.963 C=0.000, G=0.037
Allele Frequency Aggregator South Asian Sub 80 T=0.95 C=0.00, G=0.05
8.3KJPN JAPANESE Study-wide 16760 T=0.88037 G=0.11963
1000Genomes Global Study-wide 5008 T=0.7504 G=0.2496
1000Genomes African Sub 1322 T=0.6278 G=0.3722
1000Genomes East Asian Sub 1008 T=0.8938 G=0.1062
1000Genomes Europe Sub 1006 T=0.7535 G=0.2465
1000Genomes South Asian Sub 978 T=0.752 G=0.248
1000Genomes American Sub 694 T=0.769 G=0.231
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.8051 G=0.1949
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.7776 G=0.2224
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.7600 G=0.2400
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.8943 G=0.1057
HapMap Global Study-wide 1884 T=0.7261 G=0.2739
HapMap American Sub 770 T=0.771 G=0.229
HapMap African Sub 686 T=0.637 G=0.363
HapMap Asian Sub 252 T=0.849 G=0.151
HapMap Europe Sub 176 T=0.699 G=0.301
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.757 G=0.243
CNV burdens in cranial meningiomas Global Study-wide 756 T=0.917 G=0.083
CNV burdens in cranial meningiomas CRM Sub 756 T=0.917 G=0.083
Chileans Chilean Study-wide 626 T=0.736 G=0.264
Northern Sweden ACPOP Study-wide 600 T=0.777 G=0.223
Qatari Global Study-wide 216 T=0.792 G=0.208
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.901 G=0.099
SGDP_PRJ Global Study-wide 198 T=0.444 G=0.556
The Danish reference pan genome Danish Study-wide 40 T=0.75 G=0.25
Siberian Global Study-wide 20 T=0.50 G=0.50
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.p13 chr 22 NC_000022.11:g.19950010T>C
GRCh38.p13 chr 22 NC_000022.11:g.19950010T>G
GRCh37.p13 chr 22 NC_000022.10:g.19937533T>C
GRCh37.p13 chr 22 NC_000022.10:g.19937533T>G
COMT RefSeqGene (LRG_1010) NG_011526.1:g.13271T>C
COMT RefSeqGene (LRG_1010) NG_011526.1:g.13271T>G
Gene: COMT, catechol-O-methyltransferase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
COMT transcript variant 1 NM_000754.4:c.-92+8113T>C N/A Intron Variant
COMT transcript variant 5 NM_001362828.2:c.-386+811…

NM_001362828.2:c.-386+8113T>C

N/A Intron Variant
COMT transcript variant 2 NM_001135161.2:c. N/A Genic Upstream Transcript Variant
COMT transcript variant 3 NM_001135162.2:c. N/A Genic Upstream Transcript Variant
COMT transcript variant 4 NM_007310.3:c. N/A Genic Upstream Transcript 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 T= C G
GRCh38.p13 chr 22 NC_000022.11:g.19950010= NC_000022.11:g.19950010T>C NC_000022.11:g.19950010T>G
GRCh37.p13 chr 22 NC_000022.10:g.19937533= NC_000022.10:g.19937533T>C NC_000022.10:g.19937533T>G
COMT RefSeqGene (LRG_1010) NG_011526.1:g.13271= NG_011526.1:g.13271T>C NG_011526.1:g.13271T>G
COMT transcript variant 1 NM_000754.3:c.-92+8113= NM_000754.3:c.-92+8113T>C NM_000754.3:c.-92+8113T>G
COMT transcript variant 1 NM_000754.4:c.-92+8113= NM_000754.4:c.-92+8113T>C NM_000754.4:c.-92+8113T>G
COMT transcript variant 5 NM_001362828.2:c.-386+8113= NM_001362828.2:c.-386+8113T>C NM_001362828.2:c.-386+8113T>G
COMT transcript variant X1 XM_005261229.1:c.-386+8113= XM_005261229.1:c.-386+8113T>C XM_005261229.1:c.-386+8113T>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#.

61 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8287544 Apr 21, 2003 (114)
2 WI_SSAHASNP ss12523388 Jul 11, 2003 (117)
3 SSAHASNP ss21855038 Apr 05, 2004 (121)
4 ABI ss44328953 Mar 13, 2006 (126)
5 SNP500CANCER ss48293367 Mar 13, 2006 (126)
6 AFFY ss66403462 Nov 30, 2006 (127)
7 AFFY ss76154672 Dec 06, 2007 (129)
8 HGSV ss77672044 Dec 06, 2007 (129)
9 KRIBB_YJKIM ss82199674 Dec 15, 2007 (130)
10 HUMANGENOME_JCVI ss96114943 Feb 04, 2009 (130)
11 1000GENOMES ss114035850 Jan 25, 2009 (130)
12 ILLUMINA-UK ss117362025 Feb 14, 2009 (130)
13 COMPLETE_GENOMICS ss167682871 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss168891129 Jul 04, 2010 (132)
15 AFFY ss172658573 Jul 04, 2010 (132)
16 BUSHMAN ss204050407 Jul 04, 2010 (132)
17 1000GENOMES ss228618082 Jul 14, 2010 (132)
18 1000GENOMES ss238022264 Jul 15, 2010 (132)
19 1000GENOMES ss244151631 Jul 15, 2010 (132)
20 ILLUMINA ss244304016 Jul 04, 2010 (132)
21 GMI ss283587169 May 04, 2012 (137)
22 PJP ss292736288 May 09, 2011 (134)
23 TISHKOFF ss566560702 Apr 25, 2013 (138)
24 SSMP ss662483674 Apr 25, 2013 (138)
25 EVA-GONL ss995222665 Aug 21, 2014 (142)
26 JMKIDD_LAB ss1082570393 Aug 21, 2014 (142)
27 1000GENOMES ss1366682641 Aug 21, 2014 (142)
28 DDI ss1429219749 Apr 01, 2015 (144)
29 EVA_GENOME_DK ss1579704226 Apr 01, 2015 (144)
30 EVA_UK10K_ALSPAC ss1639753738 Apr 01, 2015 (144)
31 EVA_UK10K_TWINSUK ss1682747771 Apr 01, 2015 (144)
32 EVA_DECODE ss1699291778 Apr 01, 2015 (144)
33 EVA_SVP ss1713731237 Apr 01, 2015 (144)
34 HAMMER_LAB ss1809733931 Sep 08, 2015 (146)
35 WEILL_CORNELL_DGM ss1938784242 Feb 12, 2016 (147)
36 GENOMED ss1969246859 Jul 19, 2016 (147)
37 JJLAB ss2030165147 Sep 14, 2016 (149)
38 USC_VALOUEV ss2158775075 Dec 20, 2016 (150)
39 HUMAN_LONGEVITY ss2246456102 Dec 20, 2016 (150)
40 TOPMED ss2413282937 Dec 20, 2016 (150)
41 SYSTEMSBIOZJU ss2629580719 Nov 08, 2017 (151)
42 GRF ss2704518015 Nov 08, 2017 (151)
43 GNOMAD ss2972984978 Nov 08, 2017 (151)
44 AFFY ss2985850639 Nov 08, 2017 (151)
45 SWEGEN ss3019086122 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3028920282 Nov 08, 2017 (151)
47 CSHL ss3352776421 Nov 08, 2017 (151)
48 TOPMED ss3374058173 Nov 08, 2017 (151)
49 TOPMED ss3374058174 Nov 08, 2017 (151)
50 URBANLAB ss3651151842 Oct 12, 2018 (152)
51 EGCUT_WGS ss3685618672 Jul 13, 2019 (153)
52 EVA_DECODE ss3707954686 Jul 13, 2019 (153)
53 ACPOP ss3743823155 Jul 13, 2019 (153)
54 EVA ss3759230755 Jul 13, 2019 (153)
55 KHV_HUMAN_GENOMES ss3822398655 Jul 13, 2019 (153)
56 EVA ss3835927726 Apr 27, 2020 (154)
57 SGDP_PRJ ss3890256527 Apr 27, 2020 (154)
58 KRGDB ss3940640033 Apr 27, 2020 (154)
59 EVA ss3984758314 Apr 26, 2021 (155)
60 TOPMED ss5105104346 Apr 26, 2021 (155)
61 TOMMO_GENOMICS ss5232039944 Apr 26, 2021 (155)
62 1000Genomes NC_000022.10 - 19937533 Oct 12, 2018 (152)
63 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 19937533 Oct 12, 2018 (152)
64 Chileans NC_000022.10 - 19937533 Apr 27, 2020 (154)
65 Genetic variation in the Estonian population NC_000022.10 - 19937533 Oct 12, 2018 (152)
66 The Danish reference pan genome NC_000022.10 - 19937533 Apr 27, 2020 (154)
67 gnomAD - Genomes NC_000022.11 - 19950010 Apr 26, 2021 (155)
68 Genome of the Netherlands Release 5 NC_000022.10 - 19937533 Apr 27, 2020 (154)
69 HapMap NC_000022.11 - 19950010 Apr 27, 2020 (154)
70 KOREAN population from KRGDB NC_000022.10 - 19937533 Apr 27, 2020 (154)
71 Northern Sweden NC_000022.10 - 19937533 Jul 13, 2019 (153)
72 CNV burdens in cranial meningiomas NC_000022.10 - 19937533 Apr 26, 2021 (155)
73 Qatari NC_000022.10 - 19937533 Apr 27, 2020 (154)
74 SGDP_PRJ NC_000022.10 - 19937533 Apr 27, 2020 (154)
75 Siberian NC_000022.10 - 19937533 Apr 27, 2020 (154)
76 8.3KJPN NC_000022.10 - 19937533 Apr 26, 2021 (155)
77 TopMed NC_000022.11 - 19950010 Apr 26, 2021 (155)
78 UK 10K study - Twins NC_000022.10 - 19937533 Oct 12, 2018 (152)
79 A Vietnamese Genetic Variation Database NC_000022.10 - 19937533 Jul 13, 2019 (153)
80 ALFA NC_000022.11 - 19950010 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)
rs8137376 Aug 26, 2003 (117)
rs59140089 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
11767101444, ss3374058173 NC_000022.11:19950009:T:C NC_000022.11:19950009:T:C (self)
ss77672044 NC_000022.8:18312086:T:G NC_000022.11:19950009:T:G (self)
ss114035850, ss117362025, ss167682871, ss168891129, ss204050407, ss283587169, ss292736288, ss1699291778, ss1713731237 NC_000022.9:18317532:T:G NC_000022.11:19950009:T:G (self)
80217058, 44381776, 268169, 31356920, 5869165, 19773785, 47817427, 17108020, 307895, 20826164, 42273507, 11291429, 90009251, 44381776, 9792479, ss228618082, ss238022264, ss244151631, ss566560702, ss662483674, ss995222665, ss1082570393, ss1366682641, ss1429219749, ss1579704226, ss1639753738, ss1682747771, ss1809733931, ss1938784242, ss1969246859, ss2030165147, ss2158775075, ss2413282937, ss2629580719, ss2704518015, ss2972984978, ss2985850639, ss3019086122, ss3352776421, ss3685618672, ss3743823155, ss3759230755, ss3835927726, ss3890256527, ss3940640033, ss3984758314, ss5232039944 NC_000022.10:19937532:T:G NC_000022.11:19950009:T:G (self)
566540454, 2227921, 237441067, 380213293, 11767101444, ss2246456102, ss3028920282, ss3374058174, ss3651151842, ss3707954686, ss3822398655, ss5105104346 NC_000022.11:19950009:T:G NC_000022.11:19950009:T:G (self)
ss8287544, ss12523388, ss21855038, ss44328953, ss48293367, ss66403462, ss76154672, ss82199674, ss96114943, ss172658573, ss244304016 NT_011519.10:3089682:T:G NC_000022.11:19950009:T:G (self)
Help

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

12 citations for rs5993882
PMID Title Author Year Journal
16848906 Genetic polymorphisms in monoamine neurotransmitter systems show only weak association with acute post-surgical pain in humans. Kim H et al. 2006 Molecular pain
16882734 Genetic predictors for acute experimental cold and heat pain sensitivity in humans. Kim H et al. 2006 Journal of medical genetics
18574484 The complex global pattern of genetic variation and linkage disequilibrium at catechol-O-methyltransferase. Mukherjee N et al. 2010 Molecular psychiatry
19772600 A comparison of classification methods for predicting Chronic Fatigue Syndrome based on genetic data. Huang LC et al. 2009 Journal of translational medicine
20551675 Localizing putative markers in genetic association studies by incorporating linkage disequilibrium into bayesian hierarchical models. Fridley BL et al. 2010 Human heredity
21716162 Xenobiotic-metabolizing gene variants, pesticide use, and the risk of prostate cancer. Koutros S et al. 2011 Pharmacogenetics and genomics
22337325 The effect of catechol-O-methyltransferase polymorphisms on pain is modified by depressive symptoms. Schwahn C et al. 2012 European journal of pain (London, England)
24782743 Association of COMT and COMT-DRD2 interaction with creative potential. Zhang S et al. 2014 Frontiers in human neuroscience
26216165 An exploratory association study of the influence of noradrenergic genes and childhood trauma in Borderline Personality Disorder. Martín-Blanco A et al. 2015 Psychiatry research
27039372 Interaction between COMT rs5993883 and second generation antipsychotics is linked to decreases in verbal cognition and cognitive control in bipolar disorder. Flowers SA et al. 2016 BMC psychology
27247849 Genetic variation and cognitive dysfunction in opioid-treated patients with cancer. Kurita GP et al. 2016 Brain and behavior
32119983 Genetic susceptibility to parenting style: DRD2 and COMT influence creativity. Si S et al. 2020 NeuroImage
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.post676+237644a