chr16-3074919-A-G

Variant names:

• chr16-3074919-A-G
• rs4349147
• ENST00000525377.6:c.339+6680A>G

Variant summary

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

The ENST00000525377.6(IL32):​c.339+6680A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 148,442 control chromosomes in the GnomAD database, including 35,554 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 0.69 (35554 hom., cov: 24)
• Consequence: IL32 ENST00000525377.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341
• Publications: 21 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL32	ENST00000525377.6	TSL:5	c.339+6680A>G		intron	N/A	ENSP00000433866.3

Frequencies

GnomAD3 genomes AF: 0.687 AC: 101948 AN: 148352 Hom.: 35518 Cov.: 24

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.559

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.687 AC: 102039 AN: 148442 Hom.: 35554 Cov.: 24 AF XY: 0.684 AC XY: 49300 AN XY: 72038

African (AFR) AF: 0.800 AC: 32048 AN: 40070

American (AMR) AF: 0.599 AC: 8903 AN: 14860

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2171 AN: 3456

East Asian (EAS) AF: 0.539 AC: 2693 AN: 5000

South Asian (SAS) AF: 0.630 AC: 2968 AN: 4712

European-Finnish (FIN) AF: 0.652 AC: 6302 AN: 9664

Middle Eastern (MID) AF: 0.567 AC: 161 AN: 284

European-Non Finnish (NFE) AF: 0.663 AC: 44699 AN: 67440

Other (OTH) AF: 0.670 AC: 1373 AN: 2050

Alfa AF: 0.687 Hom.: 24872

Bravo AF: 0.688

Asia WGS AF: 0.600 AC: 2087 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.30
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs4349147; hg19: chr16-3124920; COSMIC: COSV73175487;