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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.

rs12252

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr11:320772 (GRCh38.p12) 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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.127300 (31738/249316, GnomAD_exome)
G=0.155223 (19491/125568, TOPMED)
G=0.124658 (15029/120562, ExAC) (+ 13 more)
G=0.13039 (4084/31322, GnomAD)
G=0.10046 (1224/12184, GO-ESP)
G=0.07176 (802/11176, ALFA Project)
G=0.2364 (1184/5008, 1000G)
G=0.0337 (130/3854, ALSPAC)
G=0.0348 (129/3708, TWINSUK)
A=0.3932 (1152/2930, KOREAN)
G=0.035 (35/998, GoNL)
G=0.033 (20/600, NorthernSweden)
G=0.009 (5/534, MGP)
A=0.360 (82/228, SGDP_PRJ)
G=0.097 (21/216, Qatari)
A=0.43 (6/14, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
IFITM3 : Synonymous Variant
Publications
34 citations
Genomic View
See rs on genome
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.p12 chr 11 NC_000011.10:g.320772A>G
GRCh37.p13 chr 11 NC_000011.9:g.320772A>G
IFITM3 RefSeqGene NG_032755.1:g.5143T>C
Gene: IFITM3, interferon induced transmembrane protein 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
IFITM3 transcript variant 1 NM_021034.3:c.42T>C S [AGT] > S [AGC] Coding Sequence Variant
interferon-induced transmembrane protein 3 NP_066362.2:p.Ser14= S (Ser) > S (Ser) Synonymous Variant
IFITM3 transcript variant 2 NR_049759.2:n.89T>C N/A Non Coding 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.

Allele: G (allele ID: 40200 )
ClinVar Accession Disease Names Clinical Significance
RCV000024238.2 Influenza Risk-Factor

ALFA Allele Frequency (New)
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 49294 A=0.93441 G=0.06559
European Sub 37272 A=0.95726 G=0.04274
African Sub 3574 A=0.7652 G=0.2348
African Others Sub 122 A=0.656 G=0.344
African American Sub 3452 A=0.7691 G=0.2309
Asian Sub 168 A=0.381 G=0.619
East Asian Sub 112 A=0.348 G=0.652
Other Asian Sub 56 A=0.45 G=0.55
Latin American 1 Sub 498 A=0.855 G=0.145
Latin American 2 Sub 628 A=0.817 G=0.183
South Asian Sub 98 A=0.86 G=0.14
Other Sub 7056 A=0.9297 G=0.0703


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 249316 A=0.872700 G=0.127300
gnomAD - Exomes European Sub 134654 A=0.954387 G=0.045613
gnomAD - Exomes Asian Sub 48562 A=0.71603 G=0.28397
gnomAD - Exomes American Sub 34516 A=0.81600 G=0.18400
gnomAD - Exomes African Sub 15472 A=0.74696 G=0.25304
gnomAD - Exomes Ashkenazi Jewish Sub 10064 A=0.90064 G=0.09936
gnomAD - Exomes Other Sub 6048 A=0.9107 G=0.0893
TopMed Global Study-wide 125568 A=0.844777 G=0.155223
ExAC Global Study-wide 120562 A=0.875342 G=0.124658
ExAC Europe Sub 73262 A=0.95341 G=0.04659
ExAC Asian Sub 25032 A=0.72767 G=0.27233
ExAC American Sub 11574 A=0.80594 G=0.19406
ExAC African Sub 9794 A=0.7503 G=0.2497
ExAC Other Sub 900 A=0.881 G=0.119
gnomAD - Genomes Global Study-wide 31322 A=0.86961 G=0.13039
gnomAD - Genomes European Sub 18882 A=0.95488 G=0.04512
gnomAD - Genomes African Sub 8672 A=0.7531 G=0.2469
gnomAD - Genomes East Asian Sub 1546 A=0.4489 G=0.5511
gnomAD - Genomes Other Sub 1084 A=0.9225 G=0.0775
gnomAD - Genomes American Sub 848 A=0.849 G=0.151
gnomAD - Genomes Ashkenazi Jewish Sub 290 A=0.907 G=0.093
GO Exome Sequencing Project Global Study-wide 12184 A=0.89954 G=0.10046
GO Exome Sequencing Project European American Sub 8288 A=0.9598 G=0.0402
GO Exome Sequencing Project African American Sub 3896 A=0.7713 G=0.2287
ALFA Total Global 11176 A=0.92824 G=0.07176
ALFA European Sub 8134 A=0.9454 G=0.0546
ALFA Other Sub 2302 A=0.9062 G=0.0938
ALFA African Sub 676 A=0.842 G=0.158
ALFA Asian Sub 60 A=0.42 G=0.58
ALFA South Asian Sub 4 A=1.0 G=0.0
ALFA Latin American 1 Sub 0 A=0 G=0
ALFA Latin American 2 Sub 0 A=0 G=0
1000Genomes Global Study-wide 5008 A=0.7636 G=0.2364
1000Genomes African Sub 1322 A=0.7398 G=0.2602
1000Genomes East Asian Sub 1008 A=0.4722 G=0.5278
1000Genomes Europe Sub 1006 A=0.9592 G=0.0408
1000Genomes South Asian Sub 978 A=0.853 G=0.147
1000Genomes American Sub 694 A=0.823 G=0.177
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9663 G=0.0337
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9652 G=0.0348
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.3932 G=0.6068
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.965 G=0.035
Northern Sweden ACPOP Study-wide 600 A=0.967 G=0.033
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.991 G=0.009
SGDP_PRJ Global Study-wide 228 A=0.360 G=0.640
Qatari Global Study-wide 216 A=0.903 G=0.097
Siberian Global Study-wide 14 A=0.43 G=0.57
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 A= G
GRCh38.p12 chr 11 NC_000011.10:g.320772= NC_000011.10:g.320772A>G
GRCh37.p13 chr 11 NC_000011.9:g.320772= NC_000011.9:g.320772A>G
IFITM3 RefSeqGene NG_032755.1:g.5143= NG_032755.1:g.5143T>C
IFITM3 transcript variant 1 NM_021034.3:c.42= NM_021034.3:c.42T>C
IFITM3 transcript variant 1 NM_021034.2:c.42= NM_021034.2:c.42T>C
IFITM3 transcript variant 2 NR_049759.2:n.89= NR_049759.2:n.89T>C
IFITM3 transcript variant 2 NR_049759.1:n.143= NR_049759.1:n.143T>C
interferon-induced transmembrane protein 3 NP_066362.2:p.Ser14= NP_066362.2:p.Ser14=
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#.

46 SubSNP, 16 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 LEE ss1542566 Oct 05, 2000 (102)
2 WI_SSAHASNP ss12125182 Jul 11, 2003 (116)
3 SC_SNP ss16145934 Feb 27, 2004 (120)
4 CGAP-GAI ss16226565 Feb 28, 2004 (124)
5 MGC_GENOME_DIFF ss28506309 Sep 24, 2004 (126)
6 MGC_GENOME_DIFF ss28512275 Sep 24, 2004 (126)
7 ABI ss46528140 Mar 11, 2006 (126)
8 HGSV ss86022479 Dec 14, 2007 (130)
9 GMI ss155798010 Dec 01, 2009 (131)
10 SEATTLESEQ ss159721906 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss168824600 Jul 04, 2010 (132)
12 1000GENOMES ss225043055 Jul 14, 2010 (132)
13 1000GENOMES ss242071197 Jul 15, 2010 (132)
14 GMI ss280846911 May 04, 2012 (137)
15 PJP ss291028516 May 09, 2011 (134)
16 CLINSEQ_SNP ss491635629 May 04, 2012 (137)
17 TISHKOFF ss562326354 Apr 25, 2013 (138)
18 SSMP ss657641885 Apr 25, 2013 (138)
19 NHLBI-ESP ss712984524 Apr 25, 2013 (138)
20 EVA-GONL ss988112719 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1067518001 Aug 21, 2014 (142)
22 1000GENOMES ss1339768741 Aug 21, 2014 (142)
23 OMIM-CURATED-RECORDS ss1505811032 Dec 08, 2014 (142)
24 EVA_UK10K_ALSPAC ss1625816589 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1668810622 Apr 01, 2015 (144)
26 EVA_EXAC ss1690159057 Apr 01, 2015 (144)
27 EVA_MGP ss1711276415 Apr 01, 2015 (144)
28 HAMMER_LAB ss1806652176 Sep 08, 2015 (146)
29 WEILL_CORNELL_DGM ss1931472844 Feb 12, 2016 (147)
30 JJLAB ss2026477062 Sep 14, 2016 (149)
31 USC_VALOUEV ss2154761423 Dec 20, 2016 (150)
32 TOPMED ss2342639874 Dec 20, 2016 (150)
33 SYSTEMSBIOZJU ss2627707704 Nov 08, 2017 (151)
34 GRF ss2699028240 Nov 08, 2017 (151)
35 GNOMAD ss2738647430 Nov 08, 2017 (151)
36 GNOMAD ss2748511174 Nov 08, 2017 (151)
37 GNOMAD ss2895348298 Nov 08, 2017 (151)
38 SWEGEN ss3007444476 Nov 08, 2017 (151)
39 TOPMED ss3134890540 Nov 08, 2017 (151)
40 OMUKHERJEE_ADBS ss3646418666 Oct 12, 2018 (152)
41 ACPOP ss3737839346 Jul 13, 2019 (153)
42 EVA ss3748833622 Jul 13, 2019 (153)
43 KHV_HUMAN_GENOMES ss3814183746 Jul 13, 2019 (153)
44 EVA ss3824572647 Apr 26, 2020 (154)
45 SGDP_PRJ ss3875445194 Apr 26, 2020 (154)
46 KRGDB ss3923657544 Apr 26, 2020 (154)
47 1000Genomes NC_000011.9 - 320772 Oct 12, 2018 (152)
48 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 320772 Oct 12, 2018 (152)
49 ExAC NC_000011.9 - 320772 Oct 12, 2018 (152)
50 gnomAD - Genomes NC_000011.9 - 320772 Jul 13, 2019 (153)
51 gnomAD - Exomes NC_000011.9 - 320772 Jul 13, 2019 (153)
52 GO Exome Sequencing Project NC_000011.9 - 320772 Oct 12, 2018 (152)
53 Genome of the Netherlands Release 5 NC_000011.9 - 320772 Apr 26, 2020 (154)
54 KOREAN population from KRGDB NC_000011.9 - 320772 Apr 26, 2020 (154)
55 Medical Genome Project healthy controls from Spanish population NC_000011.9 - 320772 Apr 26, 2020 (154)
56 Northern Sweden NC_000011.9 - 320772 Jul 13, 2019 (153)
57 Qatari NC_000011.9 - 320772 Apr 26, 2020 (154)
58 SGDP_PRJ NC_000011.9 - 320772 Apr 26, 2020 (154)
59 Siberian NC_000011.9 - 320772 Apr 26, 2020 (154)
60 TopMed NC_000011.10 - 320772 Oct 12, 2018 (152)
61 UK 10K study - Twins NC_000011.9 - 320772 Oct 12, 2018 (152)
62 dbGaP Population Frequency Project NC_000011.10 - 320772 Apr 26, 2020 (154)
63 ClinVar RCV000024238.2 Oct 12, 2018 (152)
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)
rs1059734 Jan 04, 2002 (102)
rs11539512 Dec 02, 2004 (124)
rs17852007 Mar 11, 2006 (126)
rs17857973 Mar 11, 2006 (126)
rs56885004 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss86022479, ss168824600, ss280846911, ss291028516, ss491635629 NC_000011.8:310771:A:G NC_000011.10:320771:A:G (self)
52239772, 29026057, 399554, 142685665, 7852636, 1030308, 12938018, 30834938, 392175, 11124211, 13514774, 27462174, 7277777, 29026057, ss225043055, ss242071197, ss562326354, ss657641885, ss712984524, ss988112719, ss1067518001, ss1339768741, ss1625816589, ss1668810622, ss1690159057, ss1711276415, ss1806652176, ss1931472844, ss2026477062, ss2154761423, ss2342639874, ss2627707704, ss2699028240, ss2738647430, ss2748511174, ss2895348298, ss3007444476, ss3646418666, ss3737839346, ss3748833622, ss3824572647, ss3875445194, ss3923657544 NC_000011.9:320771:A:G NC_000011.10:320771:A:G (self)
RCV000024238.2, 55207883, 112519967, ss1505811032, ss3134890540, ss3814183746 NC_000011.10:320771:A:G NC_000011.10:320771:A:G (self)
ss1542566, ss16226565, ss28506309, ss28512275, ss46528140, ss155798010, ss159721906 NT_009237.18:260771:A:G NC_000011.10:320771:A:G (self)
ss12125182 NT_035113.4:828215:T:C NC_000011.10:320771:A:G (self)
ss16145934 NT_035113.5:260771:A:G NC_000011.10:320771:A:G (self)
Help

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

34 citations for rs12252
PMID Title Author Year Journal
19946179 Identification of the polymorphisms in IFITM3 gene and their association in a Korean population with ulcerative colitis. Seo GS et al. 2010 Experimental & molecular medicine
20943977 Interferon-induced cell membrane proteins, IFITM3 and tetherin, inhibit vesicular stomatitis virus infection via distinct mechanisms. Weidner JM et al. 2010 Journal of virology
22446628 IFITM3 restricts the morbidity and mortality associated with influenza. Everitt AR et al. 2012 Nature
23361009 Interferon-induced transmembrane protein-3 genetic variant rs12252-C is associated with severe influenza in Chinese individuals. Zhang YH et al. 2013 Nature communications
23997235 IFITM3 and susceptibility to respiratory viral infections in the community. Mills TC et al. 2014 The Journal of infectious diseases
24367104 Early hypercytokinemia is associated with interferon-induced transmembrane protein-3 dysfunction and predictive of fatal H7N9 infection. Wang Z et al. 2014 Proceedings of the National Academy of Sciences of the United States of America
25314048 IFITM3 polymorphism rs12252-C restricts influenza A viruses. Williams DE et al. 2014 PloS one
25778715 IFITM3 rs12252 T>C polymorphism is associated with the risk of severe influenza: a meta-analysis. Xuan Y et al. 2015 Epidemiology and infection
25784441 Interferon-induced transmembrane protein-3 rs12252-C is associated with rapid progression of acute HIV-1 infection in Chinese MSM cohort. Zhang Y et al. 2015 AIDS (London, England)
25942469 Interferon-Inducible Transmembrane Protein 3 Genetic Variant rs12252 and Influenza Susceptibility and Severity: A Meta-Analysis. Yang X et al. 2015 PloS one
27171184 Genome-Wide Association Study Identifies Novel Susceptibility Genes Associated with Coronary Artery Aneurysm Formation in Kawasaki Disease. Kuo HC et al. 2016 PloS one
27351739 Hospitalization Risk Due to Respiratory Illness Associated with Genetic Variation at IFITM3 in Patients with Influenza A(H1N1)pdm09 Infection: A Case-Control Study. Gaio V et al. 2016 PloS one
27492307 IFITM3 and severe influenza virus infection. No evidence of genetic association. López-Rodríguez M et al. 2016 European journal of clinical microbiology & infectious diseases
28096800 Interferon-Induced Transmembrane Protein 3 Inhibits Hantaan Virus Infection, and Its Single Nucleotide Polymorphism rs12252 Influences the Severity of Hemorrhagic Fever with Renal Syndrome. Xu-Yang Z et al. 2016 Frontiers in immunology
28510725 IFITM3, TLR3, and CD55 Gene SNPs and Cumulative Genetic Risks for Severe Outcomes in Chinese Patients With H7N9/H1N1pdm09 Influenza. Lee N et al. 2017 The Journal of infectious diseases
28531322 Evaluation of IFITM3 rs12252 Association With Severe Pediatric Influenza Infection. Randolph AG et al. 2017 The Journal of infectious diseases
28713779 <i>IFITM3</i> Rs12252-C Variant Increases Potential Risk for Severe Influenza Virus Infection in Chinese Population. Pan Y et al. 2017 Frontiers in cellular and infection microbiology
28714988 SNP-mediated disruption of CTCF binding at the IFITM3 promoter is associated with risk of severe influenza in humans. Allen EK et al. 2017 Nature medicine
28813716 No Correlation of the Disease Severity of Influenza A Virus Infection with the rs12252 Polymorphism of the Interferon-Induced Transmembrane Protein 3 Gene. Kim YC et al. 2017 Intervirology
28842783 Population genetics of IFITM3 in Portugal and Central Africa reveals a potential modifier of influenza severity. David S et al. 2018 Immunogenetics
29053189 Pilot screening study of targeted genetic polymorphisms for association with seasonal influenza hospital admission. Carter TC et al. 2018 Journal of medical virology
29121968 Association of IFITM3 rs12252 polymorphisms, BMI, diabetes, and hypercholesterolemia with mild flu in an Iranian population. Mehrbod P et al. 2017 Virology journal
29202190 Lack of Truncated IFITM3 Transcripts in Cells Homozygous for the rs12252-C Variant That is Associated With Severe Influenza Infection. Makvandi-Nejad S et al. 2018 The Journal of infectious diseases
29575524 Distribution of IFITM3 polymorphism (dbSNP: rs12252) in mestizo populations in four states of Mexico. López-Jiménez JJ et al. 2018 International journal of immunogenetics
29868492 High Level Antibody Response to Pandemic Influenza H1N1/09 Virus Is Associated With Interferon-Induced Transmembrane Protein-3 rs12252-CC in Young Adults. Qin L et al. 2018 Frontiers in cellular and infection microbiology
29940276 Association between IFITM3 rs12252 polymorphism and influenza susceptibility and severity: A meta-analysis. Prabhu SS et al. 2018 Gene
30421689 Association between rs12252 and influenza susceptibility and severity: an updated meta-analysis. Chen T et al. 2018 Epidemiology and infection
30633185 Interferon-induced transmembrane protein-3 rs12252-CC is associated with low differentiation and progression of hepatocellular carcinoma. Hou Y et al. 2019 Medicine
30662816 Antiviral Protection by IFITM3 In Vivo. Zani A et al. 2018 Current clinical microbiology reports
30723081 Human megakaryocytes possess intrinsic antiviral immunity through regulated induction of IFITM3. Campbell RA et al. 2019 Blood
30987701 IFITM3: How genetics influence influenza infection demographically. Wellington D et al. 2019 Biomedical journal
31410631 Genetic characteristics and polymorphisms in the chicken interferon-induced transmembrane protein (IFITM3) gene. Kim YC et al. 2019 Veterinary research communications
31488196 Host susceptibility to severe influenza A virus infection. Clohisey S et al. 2019 Critical care (London, England)
31707755 Characteristics of H7N9 avian influenza pneumonia: a retrospective analysis of 17 cases. Yu WQ et al. 2020 Internal medicine journal
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.post565+e32b82c