ENST00000325568.9:c.-413T>A

Variant names:

• chr16-3065110-T-A
• rs28372698
• ENST00000325568.9:c.-413T>A

Variant summary

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

The ENST00000325568.9(IL32):​c.-413T>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,086 control chromosomes in the GnomAD database, including 11,696 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 0.38 (11696 hom., cov: 34)
• Consequence: IL32 ENST00000325568.9 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603
• Publications: 23 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000325568.9. 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
	IL32	ENST00000325568.9	TSL:1	c.-413T>A		upstream_gene	N/A	ENSP00000324742.5
	IL32	ENST00000531965.5	TSL:1	c.-400T>A		upstream_gene	N/A	ENSP00000433177.1
	IL32	ENST00000529699.5	TSL:1	c.-413T>A		upstream_gene	N/A	ENSP00000436937.1

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58382 AN: 151968 Hom.: 11693 Cov.: 34

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.384 AC: 58408 AN: 152086 Hom.: 11696 Cov.: 34 AF XY: 0.390 AC XY: 29011 AN XY: 74352

African (AFR) AF: 0.302 AC: 12525 AN: 41492

American (AMR) AF: 0.417 AC: 6384 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1440 AN: 3472

East Asian (EAS) AF: 0.690 AC: 3564 AN: 5166

South Asian (SAS) AF: 0.506 AC: 2438 AN: 4822

European-Finnish (FIN) AF: 0.381 AC: 4040 AN: 10590

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26619 AN: 67930

Other (OTH) AF: 0.407 AC: 860 AN: 2112

Alfa AF: 0.208 Hom.: 442

Bravo AF: 0.381

Asia WGS AF: 0.596 AC: 2071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.78
DANN	Benign	0.56
PhyloP100		-0.60
PromoterAI		0.036	Neutral

Splicing

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

Other links and lift over

dbSNP: rs28372698; hg19: chr16-3115111; COSMIC: COSV50404025;