5-132682252-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000589.4(IL4):c.361-234A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 150,096 control chromosomes in the GnomAD database, including 11,860 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 0.34 (11860 hom., cov: 31)
• Consequence: IL4 NM_000589.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554

Genes affected

IL4 (HGNC:6014): (interleukin 4) The protein encoded by this gene is a pleiotropic cytokine produced by activated T cells. This cytokine is a ligand for interleukin 4 receptor. The interleukin 4 receptor also binds to IL13, which may contribute to many overlapping functions of this cytokine and IL13. STAT6, a signal transducer and activator of transcription, has been shown to play a central role in mediating the immune regulatory signal of this cytokine. This gene, IL3, IL5, IL13, and CSF2 form a cytokine gene cluster on chromosome 5q, with this gene particularly close to IL13. This gene, IL13 and IL5 are found to be regulated coordinately by several long-range regulatory elements in an over 120 kilobase range on the chromosome. IL4 is considered an important cytokine for tissue repair, counterbalancing the effects of proinflammatory type 1 cytokines, however, it also promotes allergic airway inflammation. Moreover, IL-4, a type 2 cytokine, mediates and regulates a variety of human host responses such as allergic, anti-parasitic, wound healing, and acute inflammation. This cytokine has been reported to promote resolution of neutrophil-mediated acute lung injury. In an allergic response, IL-4 has an essential role in the production of allergen-specific immunoglobin (Ig) E. This pro-inflammatory cytokine has been observed to be increased in COVID-19 (Coronavirus disease 2019) patients, but is not necessarily associated with severe COVID-19 pathology. Two alternatively spliced transcript variants of this gene encoding distinct isoforms have been reported. [provided by RefSeq, Aug 2020]

LOC105379176 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL4	NM_000589.4	c.361-234A>G		intron_variant		ENST00000231449.7
LOC105379176	NR_134248.1	n.176+202T>C		intron_variant, non_coding_transcript_variant
IL4	NM_001354990.2	c.*51-234A>G		intron_variant
IL4	NM_172348.3	c.313-234A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL4	ENST00000231449.7	c.361-234A>G		intron_variant		1	NM_000589.4	P1
IL4	ENST00000350025.2	c.313-234A>G		intron_variant		1
IL4	ENST00000622422.1	c.*51-234A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.338 AC: 50712 AN: 149978 Hom.: 11829 Cov.: 31

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.0170

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.176

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.338 AC: 50802 AN: 150096 Hom.: 11860 Cov.: 31 AF XY: 0.346 AC XY: 25321 AN XY: 73234

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.777

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.299

Alfa AF: 0.177 Hom.: 1590

Bravo AF: 0.353

Asia WGS AF: 0.484 AC: 1685 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	0.23
Dann	Benign	0.25

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243288; hg19: chr5-132017944; COSMIC: COSV51503574; COSMIC: COSV51503574;