rs2239303

chr16-3067936-G-A

Variant summary

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

The NM_001376923.1(IL32):c.115-48G>A variant causes a intron 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 NM_001376923.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL32	NM_001376923.1	c.115-48G>A		intron_variant		ENST00000525643.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL32	ENST00000525643.7	c.115-48G>A		intron_variant		1	NM_001376923.1	A2

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

GnomAD3 exomes AF: 0.602 AC: 150810 AN: 250540 Hom.: 46329 AF XY: 0.607 AC XY: 82196 AN XY: 135456

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 SAS exome AF: 0.564

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

Gnomad4 AFR exome AF: 0.588

Gnomad4 AMR exome AF: 0.482

Gnomad4 ASJ exome AF: 0.676

Gnomad4 EAS exome AF: 0.528

Gnomad4 SAS exome AF: 0.560

Gnomad4 FIN exome AF: 0.670

Gnomad4 NFE exome AF: 0.653

Gnomad4 OTH exome AF: 0.627

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

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.622

Alfa AF: 0.643 Hom.: 31642

Bravo AF: 0.610

Asia WGS AF: 0.531 AC: 1848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.32
Dann	Benign	0.37
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Publications

LitVar

Other links and lift over

dbSNP: rs2239303; hg19: chr16-3117937; COSMIC: COSV50404028; COSMIC: COSV50404028;