16-3068864-T-C

Position:

• chr16-3068864-T-C

Variant summary

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

The NM_001376923.1(IL32):​c.202-126T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 1,461,746 control chromosomes in the GnomAD database, including 256,348 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 0.57 (24871 hom., cov: 32)
  • Exomes 𝑓: 0.59 (231477 hom.)
• Consequence: IL32 NM_001376923.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901

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]

IL32 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL32	NM_001376923.1	c.202-126T>C		intron_variant		ENST00000525643.7	NP_001363852.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL32	ENST00000525643.7	c.202-126T>C		intron_variant		1	NM_001376923.1	ENSP00000432218.3

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86416 AN: 151770 Hom.: 24857 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.580

GnomAD4 exome AF: 0.593 AC: 776633 AN: 1309858 Hom.: 231477 AF XY: 0.594 AC XY: 381466 AN XY: 642706

Gnomad4 AFR exome AF: 0.520

Gnomad4 AMR exome AF: 0.457

Gnomad4 ASJ exome AF: 0.602

Gnomad4 EAS exome AF: 0.456

Gnomad4 SAS exome AF: 0.601

Gnomad4 FIN exome AF: 0.573

Gnomad4 NFE exome AF: 0.604

Gnomad4 OTH exome AF: 0.581

GnomAD4 genome AF: 0.569 AC: 86488 AN: 151888 Hom.: 24871 Cov.: 32 AF XY: 0.567 AC XY: 42108 AN XY: 74248

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.583

Alfa AF: 0.589 Hom.: 4067

Bravo AF: 0.561

Asia WGS AF: 0.514 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.39
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs12934561; hg19: chr16-3118865; COSMIC: COSV50404254; COSMIC: COSV50404254;