rs12652920

chr5-132549548-G-C

Variant summary

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

The ENST00000450655.1(IL5):c.43-6422C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,138 control chromosomes in the GnomAD database, including 2,511 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 0.16 (2511 hom., cov: 33)
• Consequence: IL5 ENST00000450655.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89

Genes affected

IL5 (HGNC:6016): (interleukin 5) This gene encodes a cytokine that acts as a growth and differentiation factor for both B cells and eosinophils. The encoded cytokine plays a major role in the regulation of eosinophil formation, maturation, recruitment and survival. The increased production of this cytokine may be related to pathogenesis of eosinophil-dependent inflammatory diseases. This cytokine functions by binding to its receptor, which is a heterodimer, whose beta subunit is shared with the receptors for interleukine 3 (IL3) and colony stimulating factor 2 (CSF2/GM-CSF). This gene is located on chromosome 5 within a cytokine gene cluster which includes interleukin 4 (IL4), interleukin 13 (IL13), and CSF2 . This gene, IL4, and IL13 may be regulated coordinately by long-range regulatory elements spread over 120 kilobases on chromosome 5q31. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL5	XM_005271988.5	c.43-6046C>G		intron_variant
IL5	XM_011543373.4	c.-25+5608C>G		intron_variant
IL5	XM_047417148.1	c.43-6422C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL5	ENST00000450655.1	c.43-6422C>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25056 AN: 152020 Hom.: 2508 Cov.: 33

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.165 AC: 25055 AN: 152138 Hom.: 2511 Cov.: 33 AF XY: 0.167 AC XY: 12403 AN XY: 74354

Gnomad4 AFR AF: 0.0512

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.168

Alfa AF: 0.207 Hom.: 455

Bravo AF: 0.148

Asia WGS AF: 0.176 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	10
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12652920; hg19: chr5-131885240;