rs1554999

Positions:

• chr16-3065627-A-C
• chr16-3065627-A-G
• chr16-3065627-A-T

Variant summary

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

The NM_001012631.4(IL32):​c.-89A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.693 in 716,162 control chromosomes in the GnomAD database, including 175,986 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 0.72 (39964 hom., cov: 32)
  • Exomes 𝑓: 0.69 (136022 hom.)
• Consequence: IL32 NM_001012631.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL32	NM_001376923.1	c.-89A>C		upstream_gene_variant		ENST00000525643.7	NP_001363852.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL32	ENST00000525643.7	c.-89A>C		upstream_gene_variant		1	NM_001376923.1	ENSP00000432218.3

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108910 AN: 151946 Hom.: 39923 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.726

GnomAD4 exome AF: 0.687 AC: 387530 AN: 564098 Hom.: 136022 Cov.: 6 AF XY: 0.687 AC XY: 208397 AN XY: 303354

Gnomad4 AFR exome AF: 0.837

Gnomad4 AMR exome AF: 0.837

Gnomad4 ASJ exome AF: 0.658

Gnomad4 EAS exome AF: 0.963

Gnomad4 SAS exome AF: 0.729

Gnomad4 FIN exome AF: 0.603

Gnomad4 NFE exome AF: 0.639

Gnomad4 OTH exome AF: 0.687

GnomAD4 genome AF: 0.717 AC: 109010 AN: 152064 Hom.: 39964 Cov.: 32 AF XY: 0.719 AC XY: 53471 AN XY: 74328

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.939

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.726

Alfa AF: 0.654 Hom.: 31302

Bravo AF: 0.736

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.65
DANN	Benign	0.43
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs1554999; hg19: chr16-3115628;