Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs115223836

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr21:42380208 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.002252 (596/264690, TOPMED)
G=0.000561 (141/251136, GnomAD_exome)
G=0.002289 (321/140260, GnomAD) (+ 8 more)
G=0.000699 (82/117238, ExAC)
G=0.000254 (28/110188, ALFA)
G=0.00366 (288/78696, PAGE_STUDY)
G=0.00223 (29/13006, GO-ESP)
G=0.0033 (21/6404, 1000G_30x)
G=0.0034 (17/5008, 1000G)
C=0.5 (4/8, SGDP_PRJ)
G=0.5 (4/8, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
TMPRSS3 : Missense 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 110188 C=0.999746 G=0.000254
European Sub 92456 C=0.99997 G=0.00003
African Sub 4360 C=0.9952 G=0.0048
African Others Sub 174 C=1.000 G=0.000
African American Sub 4186 C=0.9950 G=0.0050
Asian Sub 3328 C=1.0000 G=0.0000
East Asian Sub 2672 C=1.0000 G=0.0000
Other Asian Sub 656 C=1.000 G=0.000
Latin American 1 Sub 790 C=0.999 G=0.001
Latin American 2 Sub 946 C=1.000 G=0.000
South Asian Sub 274 C=1.000 G=0.000
Other Sub 8034 C=0.9996 G=0.0004


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=0.997748 G=0.002252
gnomAD - Exomes Global Study-wide 251136 C=0.999439 G=0.000561
gnomAD - Exomes European Sub 135216 C=0.999993 G=0.000007
gnomAD - Exomes Asian Sub 48942 C=1.00000 G=0.00000
gnomAD - Exomes American Sub 34546 C=0.99980 G=0.00020
gnomAD - Exomes African Sub 16230 C=0.99199 G=0.00801
gnomAD - Exomes Ashkenazi Jewish Sub 10072 C=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6130 C=0.9995 G=0.0005
gnomAD - Genomes Global Study-wide 140260 C=0.997711 G=0.002289
gnomAD - Genomes European Sub 75948 C=1.00000 G=0.00000
gnomAD - Genomes African Sub 42050 C=0.99260 G=0.00740
gnomAD - Genomes American Sub 13660 C=0.99956 G=0.00044
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2148 C=0.9981 G=0.0019
ExAC Global Study-wide 117238 C=0.999301 G=0.000699
ExAC Europe Sub 71260 C=0.99999 G=0.00001
ExAC Asian Sub 24094 C=1.00000 G=0.00000
ExAC American Sub 11156 C=0.99946 G=0.00054
ExAC African Sub 9860 C=0.9924 G=0.0076
ExAC Other Sub 868 C=1.000 G=0.000
Allele Frequency Aggregator Total Global 110188 C=0.999746 G=0.000254
Allele Frequency Aggregator European Sub 92456 C=0.99997 G=0.00003
Allele Frequency Aggregator Other Sub 8034 C=0.9996 G=0.0004
Allele Frequency Aggregator African Sub 4360 C=0.9952 G=0.0048
Allele Frequency Aggregator Asian Sub 3328 C=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 946 C=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 790 C=0.999 G=0.001
Allele Frequency Aggregator South Asian Sub 274 C=1.000 G=0.000
The PAGE Study Global Study-wide 78696 C=0.99634 G=0.00366
The PAGE Study AfricanAmerican Sub 32514 C=0.99250 G=0.00750
The PAGE Study Mexican Sub 10810 C=0.99963 G=0.00037
The PAGE Study Asian Sub 8316 C=1.0000 G=0.0000
The PAGE Study PuertoRican Sub 7918 C=0.9976 G=0.0024
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 G=0.0000
The PAGE Study Cuban Sub 4230 C=0.9993 G=0.0007
The PAGE Study Dominican Sub 3828 C=0.9969 G=0.0031
The PAGE Study CentralAmerican Sub 2448 C=0.9992 G=0.0008
The PAGE Study SouthAmerican Sub 1982 C=0.9995 G=0.0005
The PAGE Study NativeAmerican Sub 1260 C=0.9976 G=0.0024
The PAGE Study SouthAsian Sub 856 C=1.000 G=0.000
GO Exome Sequencing Project Global Study-wide 13006 C=0.99777 G=0.00223
GO Exome Sequencing Project European American Sub 8600 C=1.0000 G=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9934 G=0.0066
1000Genomes_30x Global Study-wide 6404 C=0.9967 G=0.0033
1000Genomes_30x African Sub 1786 C=0.9899 G=0.0101
1000Genomes_30x Europe Sub 1266 C=1.0000 G=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 G=0.0000
1000Genomes_30x American Sub 980 C=0.997 G=0.003
1000Genomes Global Study-wide 5008 C=0.9966 G=0.0034
1000Genomes African Sub 1322 C=0.9887 G=0.0113
1000Genomes East Asian Sub 1008 C=1.0000 G=0.0000
1000Genomes Europe Sub 1006 C=1.0000 G=0.0000
1000Genomes South Asian Sub 978 C=1.000 G=0.000
1000Genomes American Sub 694 C=0.997 G=0.003
SGDP_PRJ Global Study-wide 8 C=0.5 G=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.p14 chr 21 NC_000021.9:g.42380208C>G
GRCh37.p13 chr 21 NC_000021.8:g.43800317C>G
TMPRSS3 RefSeqGene NG_011629.2:g.20884G>C
Gene: TMPRSS3, transmembrane serine protease 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
TMPRSS3 transcript variant D NM_032405.2:c. N/A Genic Downstream Transcript Variant
TMPRSS3 transcript variant F NM_001256317.3:c.957G>C M [ATG] > I [ATC] Coding Sequence Variant
transmembrane protease serine 3 isoform 4 NP_001243246.1:p.Met319Ile M (Met) > I (Ile) Missense Variant
TMPRSS3 transcript variant A NM_024022.4:c.957G>C M [ATG] > I [ATC] Coding Sequence Variant
transmembrane protease serine 3 isoform 1 NP_076927.1:p.Met319Ile M (Met) > I (Ile) Missense Variant
TMPRSS3 transcript variant C NM_032404.3:c.576G>C M [ATG] > I [ATC] Coding Sequence Variant
transmembrane protease serine 3 isoform 2 NP_115780.1:p.Met192Ile M (Met) > I (Ile) 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.

Allele: G (allele ID: 176241 )
ClinVar Accession Disease Names Clinical Significance
RCV000155296.6 not specified Benign
RCV000907877.5 not provided Benign-Likely-Benign
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= G
GRCh38.p14 chr 21 NC_000021.9:g.42380208= NC_000021.9:g.42380208C>G
GRCh37.p13 chr 21 NC_000021.8:g.43800317= NC_000021.8:g.43800317C>G
TMPRSS3 RefSeqGene NG_011629.2:g.20884= NG_011629.2:g.20884G>C
TMPRSS3 transcript variant A NM_024022.4:c.957= NM_024022.4:c.957G>C
TMPRSS3 transcript variant A NM_024022.3:c.957= NM_024022.3:c.957G>C
TMPRSS3 transcript variant A NM_024022.2:c.957= NM_024022.2:c.957G>C
TMPRSS3 transcript variant F NM_001256317.3:c.957= NM_001256317.3:c.957G>C
TMPRSS3 transcript variant F NM_001256317.2:c.957= NM_001256317.2:c.957G>C
TMPRSS3 transcript variant F NM_001256317.1:c.957= NM_001256317.1:c.957G>C
TMPRSS3 transcript variant C NM_032404.3:c.576= NM_032404.3:c.576G>C
TMPRSS3 transcript variant C NM_032404.2:c.576= NM_032404.2:c.576G>C
TMPRSS3 transcript variant G NR_046020.1:n.1913= NR_046020.1:n.1913G>C
TMPRSS3 transcript variant B NM_032401.1:c.576= NM_032401.1:c.576G>C
TADG12 transcript NM_022364.1:c.960= NM_022364.1:c.960G>C
TMPRSS3 transcript variant E NR_027348.1:n.851= NR_027348.1:n.851G>C
transmembrane protease serine 3 isoform 1 NP_076927.1:p.Met319= NP_076927.1:p.Met319Ile
transmembrane protease serine 3 isoform 4 NP_001243246.1:p.Met319= NP_001243246.1:p.Met319Ile
transmembrane protease serine 3 isoform 2 NP_115780.1:p.Met192= NP_115780.1:p.Met192Ile
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#.

43 SubSNP, 10 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss228586346 Jul 14, 2010 (132)
2 NHLBI-ESP ss342533151 May 09, 2011 (134)
3 1000GENOMES ss491185442 May 04, 2012 (137)
4 EXOME_CHIP ss491566280 May 04, 2012 (137)
5 ILLUMINA ss533641765 Sep 08, 2015 (146)
6 TISHKOFF ss566521476 Apr 25, 2013 (138)
7 ILLUMINA ss780758758 Aug 21, 2014 (142)
8 ILLUMINA ss783437487 Aug 21, 2014 (142)
9 1000GENOMES ss1366433094 Aug 21, 2014 (142)
10 EVA_EXAC ss1694166236 Apr 01, 2015 (144)
11 ILLUMINA ss1752410205 Sep 08, 2015 (146)
12 ILLUMINA ss1917951875 Feb 12, 2016 (147)
13 ILLUMINA ss1946570192 Feb 12, 2016 (147)
14 ILLUMINA ss1959957283 Feb 12, 2016 (147)
15 HUMAN_LONGEVITY ss2246072152 Dec 20, 2016 (150)
16 GNOMAD ss2744866840 Nov 08, 2017 (151)
17 GNOMAD ss2750465730 Nov 08, 2017 (151)
18 GNOMAD ss2972191478 Nov 08, 2017 (151)
19 AFFY ss2985230212 Nov 08, 2017 (151)
20 ILLUMINA ss3022163362 Nov 08, 2017 (151)
21 ILLUMINA ss3628491139 Oct 12, 2018 (152)
22 ILLUMINA ss3628491140 Oct 12, 2018 (152)
23 ILLUMINA ss3634857094 Oct 12, 2018 (152)
24 ILLUMINA ss3640564394 Oct 12, 2018 (152)
25 ILLUMINA ss3644793816 Oct 12, 2018 (152)
26 ILLUMINA ss3652623948 Oct 12, 2018 (152)
27 ILLUMINA ss3653998098 Oct 12, 2018 (152)
28 ILLUMINA ss3725951517 Jul 13, 2019 (153)
29 ILLUMINA ss3744498875 Jul 13, 2019 (153)
30 ILLUMINA ss3745156943 Jul 13, 2019 (153)
31 PAGE_CC ss3772077093 Jul 13, 2019 (153)
32 ILLUMINA ss3772652984 Jul 13, 2019 (153)
33 EVA ss3825409024 Apr 27, 2020 (154)
34 SGDP_PRJ ss3890082780 Apr 27, 2020 (154)
35 TOPMED ss5102839145 Apr 27, 2021 (155)
36 1000G_HIGH_COVERAGE ss5310346393 Oct 16, 2022 (156)
37 EVA ss5440123288 Oct 16, 2022 (156)
38 HUGCELL_USP ss5502382868 Oct 16, 2022 (156)
39 1000G_HIGH_COVERAGE ss5617547791 Oct 16, 2022 (156)
40 SANFORD_IMAGENETICS ss5664088866 Oct 16, 2022 (156)
41 EVA ss5847936036 Oct 16, 2022 (156)
42 EVA ss5892506045 Oct 16, 2022 (156)
43 EVA ss5958988199 Oct 16, 2022 (156)
44 1000Genomes NC_000021.8 - 43800317 Oct 12, 2018 (152)
45 1000Genomes_30x NC_000021.9 - 42380208 Oct 16, 2022 (156)
46 ExAC NC_000021.8 - 43800317 Oct 12, 2018 (152)
47 gnomAD - Genomes NC_000021.9 - 42380208 Apr 27, 2021 (155)
48 gnomAD - Exomes NC_000021.8 - 43800317 Jul 13, 2019 (153)
49 GO Exome Sequencing Project NC_000021.8 - 43800317 Oct 12, 2018 (152)
50 The PAGE Study NC_000021.9 - 42380208 Jul 13, 2019 (153)
51 SGDP_PRJ NC_000021.8 - 43800317 Apr 27, 2020 (154)
52 TopMed NC_000021.9 - 42380208 Apr 27, 2021 (155)
53 ALFA NC_000021.9 - 42380208 Apr 27, 2021 (155)
54 ClinVar RCV000155296.6 Oct 16, 2022 (156)
55 ClinVar RCV000907877.5 Oct 16, 2022 (156)
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
79958427, 5733718, 14193444, 1865896, 42099760, ss228586346, ss342533151, ss491185442, ss491566280, ss533641765, ss566521476, ss780758758, ss783437487, ss1366433094, ss1694166236, ss1752410205, ss1917951875, ss1946570192, ss1959957283, ss2744866840, ss2750465730, ss2972191478, ss2985230212, ss3022163362, ss3628491139, ss3628491140, ss3634857094, ss3640564394, ss3644793816, ss3652623948, ss3653998098, ss3744498875, ss3745156943, ss3772652984, ss3825409024, ss3890082780, ss5440123288, ss5664088866, ss5847936036, ss5958988199 NC_000021.8:43800316:C:G NC_000021.9:42380207:C:G (self)
RCV000155296.6, RCV000907877.5, 105073726, 564191201, 1298562, 377948091, 5930524908, ss2246072152, ss3725951517, ss3772077093, ss5102839145, ss5310346393, ss5502382868, ss5617547791, ss5892506045 NC_000021.9:42380207:C:G NC_000021.9:42380207:C:G (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 rs115223836
PMID Title Author Year Journal
24033266 A systematic approach to assessing the clinical significance of genetic variants. Duzkale H et al. 2013 Clinical genetics
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.post761+d5e8e07