rs3024647

Variant names:

• chr16-27356651-G-A
• rs3024647
• NM_000418.4:c.770+744G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000418.4(IL4R):​c.770+744G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 151,972 control chromosomes in the GnomAD database, including 48,814 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 0.79 (48814 hom., cov: 30)
• Consequence: IL4R NM_000418.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.748
• Publications: 12 publications found

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]

IL4R Gene-Disease associations (from GenCC):

• IgE responsiveness, atopic

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL4R	NM_000418.4	c.770+744G>A		intron_variant	Intron 8 of 10	ENST00000395762.7	NP_000409.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL4R	ENST00000395762.7	c.770+744G>A		intron_variant	Intron 8 of 10	1	NM_000418.4	ENSP00000379111.2

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120380 AN: 151854 Hom.: 48789 Cov.: 30

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.984

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.823

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.793 AC: 120458 AN: 151972 Hom.: 48814 Cov.: 30 AF XY: 0.796 AC XY: 59120 AN XY: 74286

African (AFR) AF: 0.613 AC: 25357 AN: 41384

American (AMR) AF: 0.865 AC: 13201 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2974 AN: 3470

East Asian (EAS) AF: 0.912 AC: 4702 AN: 5158

South Asian (SAS) AF: 0.888 AC: 4273 AN: 4812

European-Finnish (FIN) AF: 0.841 AC: 8888 AN: 10570

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58176 AN: 67992

Other (OTH) AF: 0.825 AC: 1742 AN: 2112

Alfa AF: 0.822 Hom.: 15691

Bravo AF: 0.788

Asia WGS AF: 0.873 AC: 3036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.37
PhyloP100		-0.75
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3024647; hg19: chr16-27367972;