rs2074570
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000418.4(IL4R):c.*6T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0528 in 1,596,006 control chromosomes in the GnomAD database, including 3,385 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.090 ( 917 hom., cov: 33)
Exomes 𝑓: 0.049 ( 2468 hom. )
Consequence
IL4R
NM_000418.4 3_prime_UTR
NM_000418.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.722
Genes affected
IL4R (HGNC:6015): (interleukin 4 receptor) This gene encodes the alpha chain of the interleukin-4 receptor, a type I transmembrane protein that can bind interleukin 4 and interleukin 13 to regulate IgE production. The encoded protein also can bind interleukin 4 to promote differentiation of Th2 cells. A soluble form of the encoded protein can be produced by proteolysis of the membrane-bound protein, and this soluble form can inhibit IL4-mediated cell proliferation and IL5 upregulation by T-cells. Allelic variations in this gene have been associated with atopy, a condition that can manifest itself as allergic rhinitis, sinusitus, asthma, or eczema. Polymorphisms in this gene are also associated with resistance to human immunodeficiency virus type-1 infection. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Apr 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 16-27363836-T-C is Benign according to our data. Variant chr16-27363836-T-C is described in ClinVar as [Benign]. Clinvar id is 3059990.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL4R | NM_000418.4 | c.*6T>C | 3_prime_UTR_variant | 11/11 | ENST00000395762.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL4R | ENST00000395762.7 | c.*6T>C | 3_prime_UTR_variant | 11/11 | 1 | NM_000418.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0900 AC: 13692AN: 152188Hom.: 912 Cov.: 33
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GnomAD3 exomes AF: 0.0720 AC: 16779AN: 233168Hom.: 872 AF XY: 0.0666 AC XY: 8467AN XY: 127100
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GnomAD4 exome AF: 0.0488 AC: 70487AN: 1443700Hom.: 2468 Cov.: 33 AF XY: 0.0492 AC XY: 35306AN XY: 718132
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GnomAD4 genome ? AF: 0.0901 AC: 13720AN: 152306Hom.: 917 Cov.: 33 AF XY: 0.0921 AC XY: 6860AN XY: 74472
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
IL4R-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at