ENST00000532247.5:n.652G>A

Variant names:

• chr16-3067936-G-A
• rs2239303
• ENST00000532247.5:n.652G>A

Variant summary

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

The ENST00000532247.5(IL32):​n.652G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 1,605,396 control chromosomes in the GnomAD database, including 326,550 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 0.62 (29443 hom., cov: 32)
  • Exomes 𝑓: 0.64 (297107 hom.)
• Consequence: IL32 ENST00000532247.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 14 publications found

Genes affected

IL32 (HGNC:16830): (interleukin 32) This gene encodes a member of the cytokine family. The protein contains a tyrosine sulfation site, 3 potential N-myristoylation sites, multiple putative phosphorylation sites, and an RGD cell-attachment sequence. Expression of this protein is increased after the activation of T-cells by mitogens or the activation of NK cells by IL-2. This protein induces the production of TNFalpha from macrophage cells. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532247.5. 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
	IL32	NM_001376923.1	MANE Select	c.115-48G>A		intron	N/A	NP_001363852.1
	IL32	NM_001308078.4		c.253-48G>A		intron	N/A	NP_001295007.1
	IL32	NM_001369587.3		c.253-48G>A		intron	N/A	NP_001356516.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL32	ENST00000532247.5	TSL:1	n.652G>A		non_coding_transcript_exon	Exon 3 of 3
	IL32	ENST00000525643.7	TSL:1 MANE Select	c.115-48G>A		intron	N/A	ENSP00000432218.3
	IL32	ENST00000396890.6	TSL:1	c.253-48G>A		intron	N/A	ENSP00000380099.2

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94234 AN: 151908 Hom.: 29419 Cov.: 32

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.621

GnomAD2 exomes AF: 0.602 AC: 150810 AN: 250540 AF XY: 0.607

Gnomad AFR exome AF: 0.587

Gnomad AMR exome AF: 0.471

Gnomad ASJ exome AF: 0.674

Gnomad EAS exome AF: 0.455

Gnomad FIN exome AF: 0.674

Gnomad NFE exome AF: 0.657

Gnomad OTH exome AF: 0.613

GnomAD4 exome AF: 0.637 AC: 925819 AN: 1453368 Hom.: 297107 Cov.: 31 AF XY: 0.636 AC XY: 460153 AN XY: 723586

African (AFR) AF: 0.588 AC: 19575 AN: 33302

American (AMR) AF: 0.482 AC: 21515 AN: 44664

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 17630 AN: 26080

East Asian (EAS) AF: 0.528 AC: 20950 AN: 39650

South Asian (SAS) AF: 0.560 AC: 48169 AN: 86056

European-Finnish (FIN) AF: 0.670 AC: 35799 AN: 53394

Middle Eastern (MID) AF: 0.592 AC: 3406 AN: 5752

European-Non Finnish (NFE) AF: 0.653 AC: 721117 AN: 1104390

Other (OTH) AF: 0.627 AC: 37658 AN: 60080

GnomAD4 genome AF: 0.620 AC: 94313 AN: 152028 Hom.: 29443 Cov.: 32 AF XY: 0.620 AC XY: 46051 AN XY: 74318

African (AFR) AF: 0.588 AC: 24365 AN: 41448

American (AMR) AF: 0.549 AC: 8407 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2355 AN: 3472

East Asian (EAS) AF: 0.482 AC: 2489 AN: 5166

South Asian (SAS) AF: 0.564 AC: 2721 AN: 4826

European-Finnish (FIN) AF: 0.679 AC: 7180 AN: 10580

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44639 AN: 67922

Other (OTH) AF: 0.622 AC: 1313 AN: 2112

Alfa AF: 0.637 Hom.: 45836

Bravo AF: 0.610

Asia WGS AF: 0.531 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.37
PhyloP100		-1.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2239303; hg19: chr16-3117937; COSMIC: COSV50404028; COSMIC: COSV50404028;