rs12652920

Variant names:

• chr5-132549548-G-C
• rs12652920
• ENST00000638452.2:c.-168-9736G>C

Variant summary

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

The ENST00000638452.2(ENSG00000283782):​c.-168-9736G>C 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: ENSG00000283782 ENST00000638452.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 15 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283782	ENST00000638452.2	TSL:5	c.-168-9736G>C		intron	N/A	ENSP00000492349.2	A0A1W2PQ90
	ENSG00000283782	ENST00000638568.2	TSL:5	c.-310-6784G>C		intron	N/A	ENSP00000491158.2	A0A1W2PQ90
	ENSG00000283782	ENST00000640655.2	TSL:5	c.-168-9736G>C		intron	N/A	ENSP00000491596.2	A0A1W2PQ90

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

African (AFR) AF: 0.0512 AC: 2125 AN: 41544

American (AMR) AF: 0.145 AC: 2222 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 772 AN: 3470

East Asian (EAS) AF: 0.176 AC: 912 AN: 5184

South Asian (SAS) AF: 0.209 AC: 1006 AN: 4816

European-Finnish (FIN) AF: 0.250 AC: 2635 AN: 10554

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14856 AN: 67964

Other (OTH) AF: 0.168 AC: 354 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.54
PhyloP100		1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12652920;

hg19: chr5-131885240;