NM_000586.4:c.-476T>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_000586.4(IL2):c.-476T>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.986 in 152,080 control chromosomes in the GnomAD database, including 73,909 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.99 ( 73909 hom., cov: 32)
Consequence
IL2
NM_000586.4 upstream_gene
NM_000586.4 upstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.09
Publications
4 publications found
Genes affected
IL2 (HGNC:6001): (interleukin 2) This gene is a member of the interleukin 2 (IL2) cytokine subfamily which includes IL4, IL7, IL9, IL15, IL21, erythropoietin, and thrombopoietin. The protein encoded by this gene is a secreted cytokine produced by activated CD4+ and CD8+ T lymphocytes, that is important for the proliferation of T and B lymphocytes. The receptor of this cytokine (IL2R) is a heterotrimeric protein complex whose gamma chain is also shared by IL4 and IL7. The expression of this gene in mature thymocytes is monoallelic, which represents an unusual regulatory mode for controlling the precise expression of a single gene. The targeted disruption of a similar gene in mice leads to ulcerative colitis-like disease, which suggests an essential role of this gene in the immune response to antigenic stimuli. [provided by RefSeq, Sep 2020]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.986 AC: 149782AN: 151962Hom.: 73854 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
149782
AN:
151962
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.986 AC: 149897AN: 152080Hom.: 73909 Cov.: 32 AF XY: 0.986 AC XY: 73333AN XY: 74362 show subpopulations
GnomAD4 genome
AF:
AC:
149897
AN:
152080
Hom.:
Cov.:
32
AF XY:
AC XY:
73333
AN XY:
74362
show subpopulations
African (AFR)
AF:
AC:
39459
AN:
41510
American (AMR)
AF:
AC:
15145
AN:
15226
Ashkenazi Jewish (ASJ)
AF:
AC:
3468
AN:
3468
East Asian (EAS)
AF:
AC:
5179
AN:
5180
South Asian (SAS)
AF:
AC:
4826
AN:
4826
European-Finnish (FIN)
AF:
AC:
10624
AN:
10624
Middle Eastern (MID)
AF:
AC:
293
AN:
294
European-Non Finnish (NFE)
AF:
AC:
67908
AN:
67934
Other (OTH)
AF:
AC:
2085
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
105
211
316
422
527
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
914
1828
2742
3656
4570
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3463
AN:
3472
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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