16-3073560-A-T

Position:

• chr16-3073560-A-T

Variant summary

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

The ENST00000525377.6(IL32):​c.339+5321A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,880 control chromosomes in the GnomAD database, including 25,175 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 0.56 (25175 hom., cov: 31)
• Consequence: IL32 ENST00000525377.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL32	ENST00000525377.6	c.339+5321A>T		intron_variant		5		ENSP00000433866	A2

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84836 AN: 151762 Hom.: 25156 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.531

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.559 AC: 84905 AN: 151880 Hom.: 25175 Cov.: 31 AF XY: 0.560 AC XY: 41581 AN XY: 74214

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.571

Alfa AF: 0.598 Hom.: 3351

Bravo AF: 0.539

Asia WGS AF: 0.568 AC: 1976 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	0.67
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2015620; hg19: chr16-3123561;