chr16-3065627-A-C

Variant names:

• chr16-3065627-A-C
• rs1554999
• ENST00000532086.1:n.273A>C

Variant summary

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

The ENST00000532086.1(IL32):​n.273A>C variant causes a non coding transcript exon 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 ENST00000532086.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 26 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=-0.88).
• 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 rank	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 rank	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

African (AFR) AF: 0.837 AC: 13130 AN: 15692

American (AMR) AF: 0.837 AC: 28443 AN: 33980

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 10796 AN: 16404

East Asian (EAS) AF: 0.963 AC: 34193 AN: 35490

South Asian (SAS) AF: 0.729 AC: 42240 AN: 57970

European-Finnish (FIN) AF: 0.603 AC: 26786 AN: 44442

Middle Eastern (MID) AF: 0.791 AC: 2155 AN: 2724

European-Non Finnish (NFE) AF: 0.639 AC: 209012 AN: 327142

Other (OTH) AF: 0.687 AC: 20775 AN: 30254

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

African (AFR) AF: 0.833 AC: 34576 AN: 41496

American (AMR) AF: 0.791 AC: 12093 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2359 AN: 3470

East Asian (EAS) AF: 0.939 AC: 4856 AN: 5172

South Asian (SAS) AF: 0.736 AC: 3550 AN: 4822

European-Finnish (FIN) AF: 0.592 AC: 6246 AN: 10558

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43011 AN: 67952

Other (OTH) AF: 0.726 AC: 1530 AN: 2106

Alfa AF: 0.664 Hom.: 45172

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
PhyloP100		-1.9
PromoterAI		0.17	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1554999; hg19: chr16-3115628;