16-3066185-T-G

Variant names:

• chr16-3066185-T-G
• rs9927163
• NM_001376923.1:c.15+359T>G

Variant summary

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

The NM_001376923.1(IL32):​c.15+359T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 151,930 control chromosomes in the GnomAD database, including 18,789 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 0.47 (18789 hom., cov: 32)
• Consequence: IL32 NM_001376923.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001376923.1. 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
	IL32	NM_001376923.1	MANE Select	c.15+359T>G		intron	N/A	NP_001363852.1
	IL32	NM_001308078.4		c.15+359T>G		intron	N/A	NP_001295007.1
	IL32	NM_001369587.3		c.15+359T>G		intron	N/A	NP_001356516.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL32	ENST00000525643.7	TSL:1 MANE Select	c.15+359T>G		intron	N/A	ENSP00000432218.3
	IL32	ENST00000396890.6	TSL:1	c.15+359T>G		intron	N/A	ENSP00000380099.2
	IL32	ENST00000325568.9	TSL:1	c.15+359T>G		intron	N/A	ENSP00000324742.5

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71136 AN: 151810 Hom.: 18740 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.469 AC: 71248 AN: 151930 Hom.: 18789 Cov.: 32 AF XY: 0.476 AC XY: 35356 AN XY: 74272

African (AFR) AF: 0.619 AC: 25622 AN: 41408

American (AMR) AF: 0.570 AC: 8702 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1282 AN: 3468

East Asian (EAS) AF: 0.975 AC: 5009 AN: 5140

South Asian (SAS) AF: 0.544 AC: 2620 AN: 4816

European-Finnish (FIN) AF: 0.344 AC: 3637 AN: 10578

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22938 AN: 67936

Other (OTH) AF: 0.472 AC: 995 AN: 2108

Alfa AF: 0.384 Hom.: 17034

Bravo AF: 0.493

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.32
PhyloP100		-0.62
PromoterAI		0.039	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs9927163; hg19: chr16-3116186;