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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.

rs9332316

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr22:19942751 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.010658 (2821/264690, TOPMED)
T=0.015857 (2265/142842, ALFA)
T=0.010787 (1513/140262, GnomAD) (+ 12 more)
T=0.0064 (32/5008, 1000G)
T=0.0074 (33/4480, Estonian)
T=0.0158 (61/3854, ALSPAC)
T=0.0148 (55/3708, TWINSUK)
T=0.0003 (1/2922, KOREAN)
T=0.015 (15/998, GoNL)
T=0.023 (18/778, HapMap)
T=0.028 (17/600, NorthernSweden)
T=0.019 (4/216, Qatari)
T=0.03 (1/40, GENOME_DK)
C=0.5 (3/6, SGDP_PRJ)
T=0.5 (3/6, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
COMT : Intron Variant
TXNRD2 : 2KB Upstream 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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 142842 C=0.984143 T=0.015857
European Sub 126214 C=0.983053 T=0.016947
African Sub 6678 C=0.9967 T=0.0033
African Others Sub 242 C=1.000 T=0.000
African American Sub 6436 C=0.9966 T=0.0034
Asian Sub 630 C=1.000 T=0.000
East Asian Sub 498 C=1.000 T=0.000
Other Asian Sub 132 C=1.000 T=0.000
Latin American 1 Sub 692 C=0.991 T=0.009
Latin American 2 Sub 2264 C=0.9920 T=0.0080
South Asian Sub 184 C=1.000 T=0.000
Other Sub 6180 C=0.9871 T=0.0129


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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.989342 T=0.010658
Allele Frequency Aggregator Total Global 142842 C=0.984143 T=0.015857
Allele Frequency Aggregator European Sub 126214 C=0.983053 T=0.016947
Allele Frequency Aggregator African Sub 6678 C=0.9967 T=0.0033
Allele Frequency Aggregator Other Sub 6180 C=0.9871 T=0.0129
Allele Frequency Aggregator Latin American 2 Sub 2264 C=0.9920 T=0.0080
Allele Frequency Aggregator Latin American 1 Sub 692 C=0.991 T=0.009
Allele Frequency Aggregator Asian Sub 630 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 184 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 140262 C=0.989213 T=0.010787
gnomAD - Genomes European Sub 75954 C=0.98514 T=0.01486
gnomAD - Genomes African Sub 42038 C=0.99707 T=0.00293
gnomAD - Genomes American Sub 13662 C=0.99019 T=0.00981
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.9705 T=0.0295
gnomAD - Genomes East Asian Sub 3130 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=0.9865 T=0.0135
1000Genomes Global Study-wide 5008 C=0.9936 T=0.0064
1000Genomes African Sub 1322 C=0.9985 T=0.0015
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9831 T=0.0169
1000Genomes South Asian Sub 978 C=0.998 T=0.002
1000Genomes American Sub 694 C=0.984 T=0.016
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9926 T=0.0074
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9842 T=0.0158
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9852 T=0.0148
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9997 T=0.0003
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.985 T=0.015
HapMap Global Study-wide 778 C=0.977 T=0.023
HapMap American Sub 424 C=0.979 T=0.021
HapMap African Sub 178 C=0.994 T=0.006
HapMap Europe Sub 176 C=0.955 T=0.045
Northern Sweden ACPOP Study-wide 600 C=0.972 T=0.028
Qatari Global Study-wide 216 C=0.981 T=0.019
The Danish reference pan genome Danish Study-wide 40 C=0.97 T=0.03
SGDP_PRJ Global Study-wide 6 C=0.5 T=0.5
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.19942751C>T
GRCh37.p13 chr 22 NC_000022.10:g.19930274C>T
TXNRD2 RefSeqGene (LRG_417) NG_011835.1:g.4086G>A
COMT RefSeqGene (LRG_1010) NG_011526.1:g.6012C>T
Gene: COMT, catechol-O-methyltransferase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
COMT transcript variant 1 NM_000754.4:c.-92+854C>T N/A Intron Variant
COMT transcript variant 5 NM_001362828.2:c.-386+854…

NM_001362828.2:c.-386+854C>T

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
Gene: TXNRD2, thioredoxin reductase 2 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
TXNRD2 transcript variant 5 NM_001282512.3:c. N/A Upstream Transcript Variant
TXNRD2 transcript variant 2 NM_001352300.2:c. N/A Upstream Transcript Variant
TXNRD2 transcript variant 1 NM_006440.5:c. N/A Upstream Transcript Variant
TXNRD2 transcript variant 3 NM_001352301.2:c. N/A N/A
TXNRD2 transcript variant 4 NM_001352302.2:c. N/A N/A
TXNRD2 transcript variant 6 NM_001352303.2:c. N/A N/A
TXNRD2 transcript variant 7 NR_147957.2:n. N/A 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 C= T
GRCh38.p13 chr 22 NC_000022.11:g.19942751= NC_000022.11:g.19942751C>T
GRCh37.p13 chr 22 NC_000022.10:g.19930274= NC_000022.10:g.19930274C>T
TXNRD2 RefSeqGene (LRG_417) NG_011835.1:g.4086= NG_011835.1:g.4086G>A
COMT RefSeqGene (LRG_1010) NG_011526.1:g.6012= NG_011526.1:g.6012C>T
COMT transcript variant 1 NM_000754.3:c.-92+854= NM_000754.3:c.-92+854C>T
COMT transcript variant 1 NM_000754.4:c.-92+854= NM_000754.4:c.-92+854C>T
COMT transcript variant 5 NM_001362828.2:c.-386+854= NM_001362828.2:c.-386+854C>T
COMT transcript variant X1 XM_005261229.1:c.-386+854= XM_005261229.1:c.-386+854C>T
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#.

52 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss12673697 Dec 05, 2003 (119)
2 ILLUMINA ss75104587 Dec 07, 2007 (129)
3 KRIBB_YJKIM ss119589413 Dec 01, 2009 (131)
4 ILLUMINA ss160978177 Dec 01, 2009 (131)
5 ILLUMINA ss174814815 Jul 04, 2010 (132)
6 1000GENOMES ss238022241 Jul 15, 2010 (132)
7 ILLUMINA ss481871376 May 04, 2012 (137)
8 ILLUMINA ss481904157 May 04, 2012 (137)
9 ILLUMINA ss482863160 Sep 08, 2015 (146)
10 ILLUMINA ss485729894 May 04, 2012 (137)
11 ILLUMINA ss537588088 Sep 08, 2015 (146)
12 ILLUMINA ss779007129 Sep 08, 2015 (146)
13 ILLUMINA ss783310642 Sep 08, 2015 (146)
14 ILLUMINA ss784262768 Sep 08, 2015 (146)
15 ILLUMINA ss832572089 Sep 08, 2015 (146)
16 ILLUMINA ss834469558 Sep 08, 2015 (146)
17 EVA-GONL ss995222588 Aug 21, 2014 (142)
18 1000GENOMES ss1366682431 Aug 21, 2014 (142)
19 EVA_GENOME_DK ss1579704199 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1639753625 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1682747658 Apr 01, 2015 (144)
22 EVA_DECODE ss1699291712 Apr 01, 2015 (144)
23 EVA_SVP ss1713731229 Apr 01, 2015 (144)
24 ILLUMINA ss1752413944 Sep 08, 2015 (146)
25 WEILL_CORNELL_DGM ss1938784176 Feb 12, 2016 (147)
26 JJLAB ss2030165113 Sep 14, 2016 (149)
27 HUMAN_LONGEVITY ss2246455625 Dec 20, 2016 (150)
28 TOPMED ss2413282483 Dec 20, 2016 (150)
29 ILLUMINA ss2633862726 Nov 08, 2017 (151)
30 GNOMAD ss2972984374 Nov 08, 2017 (151)
31 SWEGEN ss3019086018 Nov 08, 2017 (151)
32 TOPMED ss3374056883 Nov 08, 2017 (151)
33 ILLUMINA ss3628505957 Oct 12, 2018 (152)
34 ILLUMINA ss3631815132 Oct 12, 2018 (152)
35 ILLUMINA ss3633268840 Oct 12, 2018 (152)
36 ILLUMINA ss3633984228 Oct 12, 2018 (152)
37 ILLUMINA ss3634860916 Oct 12, 2018 (152)
38 ILLUMINA ss3635668867 Oct 12, 2018 (152)
39 ILLUMINA ss3636556551 Oct 12, 2018 (152)
40 ILLUMINA ss3637421058 Oct 12, 2018 (152)
41 ILLUMINA ss3638374413 Oct 12, 2018 (152)
42 ILLUMINA ss3640568217 Oct 12, 2018 (152)
43 ILLUMINA ss3643334824 Oct 12, 2018 (152)
44 EGCUT_WGS ss3685618570 Jul 13, 2019 (153)
45 EVA_DECODE ss3707954572 Jul 13, 2019 (153)
46 ACPOP ss3743823087 Jul 13, 2019 (153)
47 ILLUMINA ss3745160748 Jul 13, 2019 (153)
48 ILLUMINA ss3772656732 Jul 13, 2019 (153)
49 SGDP_PRJ ss3890256412 Apr 27, 2020 (154)
50 KRGDB ss3940639892 Apr 27, 2020 (154)
51 EVA ss4017873631 Apr 26, 2021 (155)
52 TOPMED ss5105102587 Apr 26, 2021 (155)
53 1000Genomes NC_000022.10 - 19930274 Oct 12, 2018 (152)
54 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 19930274 Oct 12, 2018 (152)
55 Genetic variation in the Estonian population NC_000022.10 - 19930274 Oct 12, 2018 (152)
56 The Danish reference pan genome NC_000022.10 - 19930274 Apr 27, 2020 (154)
57 gnomAD - Genomes NC_000022.11 - 19942751 Apr 26, 2021 (155)
58 Genome of the Netherlands Release 5 NC_000022.10 - 19930274 Apr 27, 2020 (154)
59 HapMap NC_000022.11 - 19942751 Apr 27, 2020 (154)
60 KOREAN population from KRGDB NC_000022.10 - 19930274 Apr 27, 2020 (154)
61 Northern Sweden NC_000022.10 - 19930274 Jul 13, 2019 (153)
62 Qatari NC_000022.10 - 19930274 Apr 27, 2020 (154)
63 SGDP_PRJ NC_000022.10 - 19930274 Apr 27, 2020 (154)
64 TopMed NC_000022.11 - 19942751 Apr 26, 2021 (155)
65 UK 10K study - Twins NC_000022.10 - 19930274 Oct 12, 2018 (152)
66 ALFA NC_000022.11 - 19942751 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
ss481871376, ss1699291712, ss1713731229, ss3643334824 NC_000022.9:18310273:C:T NC_000022.11:19942750:C:T (self)
80216842, 44381656, 31356818, 5869138, 19773710, 47817286, 17107952, 20826098, 42273392, 44381656, ss238022241, ss481904157, ss482863160, ss485729894, ss537588088, ss779007129, ss783310642, ss784262768, ss832572089, ss834469558, ss995222588, ss1366682431, ss1579704199, ss1639753625, ss1682747658, ss1752413944, ss1938784176, ss2030165113, ss2413282483, ss2633862726, ss2972984374, ss3019086018, ss3628505957, ss3631815132, ss3633268840, ss3633984228, ss3634860916, ss3635668867, ss3636556551, ss3637421058, ss3638374413, ss3640568217, ss3685618570, ss3743823087, ss3745160748, ss3772656732, ss3890256412, ss3940639892, ss4017873631 NC_000022.10:19930273:C:T NC_000022.11:19942750:C:T (self)
566538991, 2227912, 237439960, 380211534, 7902712537, ss2246455625, ss3374056883, ss3707954572, ss5105102587 NC_000022.11:19942750:C:T NC_000022.11:19942750:C:T (self)
ss12673697, ss75104587, ss119589413, ss160978177, ss174814815 NT_011519.10:3082423:C:T NC_000022.11:19942750: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.

No publications for rs9332316

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