ENST00000525377.6:c.339+4042G>A

Variant names:

• chr16-3072281-G-A
• rs12447486
• ENST00000525377.6:c.339+4042G>A

Variant summary

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

The ENST00000525377.6(IL32):​c.339+4042G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 147,240 control chromosomes in the GnomAD database, including 19,744 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 0.51 (19744 hom., cov: 29)
• Consequence: IL32 ENST00000525377.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525377.6. 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	ENST00000525377.6	TSL:5	c.339+4042G>A		intron	N/A	ENSP00000433866.3

Frequencies

GnomAD3 genomes AF: 0.508 AC: 74733 AN: 147128 Hom.: 19740 Cov.: 29

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.508 AC: 74769 AN: 147240 Hom.: 19744 Cov.: 29 AF XY: 0.508 AC XY: 36542 AN XY: 71912

African (AFR) AF: 0.282 AC: 11447 AN: 40596

American (AMR) AF: 0.488 AC: 7244 AN: 14836

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 1949 AN: 3318

East Asian (EAS) AF: 0.388 AC: 1963 AN: 5060

South Asian (SAS) AF: 0.586 AC: 2724 AN: 4652

European-Finnish (FIN) AF: 0.634 AC: 6504 AN: 10258

Middle Eastern (MID) AF: 0.507 AC: 145 AN: 286

European-Non Finnish (NFE) AF: 0.629 AC: 41077 AN: 65332

Other (OTH) AF: 0.522 AC: 1065 AN: 2042

Alfa AF: 0.415 Hom.: 967

Asia WGS AF: 0.465 AC: 1620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.31
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs12447486; hg19: chr16-3122282; COSMIC: COSV50405602;