5-132548075-A-T

Variant names:

• chr5-132548075-A-T
• rs2522411
• ENST00000638452.2:c.-168-11209A>T

Variant summary

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

The ENST00000638452.2(ENSG00000283782):​c.-168-11209A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 151,922 control chromosomes in the GnomAD database, including 37,150 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 0.68 (37150 hom., cov: 31)
• Consequence: ENSG00000283782 ENST00000638452.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 8 publications found

Genes affected

ENSG00000283782 (HGNC:):

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638452.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283782	ENST00000638452.2	TSL:5	c.-168-11209A>T		intron	N/A	ENSP00000492349.2
	ENSG00000283782	ENST00000638568.2	TSL:5	c.-310-8257A>T		intron	N/A	ENSP00000491158.2
	ENSG00000283782	ENST00000640655.2	TSL:5	c.-168-11209A>T		intron	N/A	ENSP00000491596.2

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103435 AN: 151804 Hom.: 37140 Cov.: 31

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.681 AC: 103466 AN: 151922 Hom.: 37150 Cov.: 31 AF XY: 0.683 AC XY: 50733 AN XY: 74254

African (AFR) AF: 0.427 AC: 17660 AN: 41356

American (AMR) AF: 0.794 AC: 12127 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2654 AN: 3470

East Asian (EAS) AF: 0.822 AC: 4260 AN: 5180

South Asian (SAS) AF: 0.761 AC: 3665 AN: 4816

European-Finnish (FIN) AF: 0.750 AC: 7904 AN: 10536

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52644 AN: 67986

Other (OTH) AF: 0.728 AC: 1537 AN: 2110

Alfa AF: 0.698 Hom.: 4720

Bravo AF: 0.675

Asia WGS AF: 0.772 AC: 2678 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
DANN	Benign	0.29
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2522411; hg19: chr5-131883767;