16-3074919-A-G

Position:

• chr16-3074919-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL32	ENST00000525377.6	c.339+6680A>G		intron_variant		5		ENSP00000433866	A2

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

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.670

Alfa AF: 0.669 Hom.: 13508

Bravo AF: 0.688

Asia WGS AF: 0.600 AC: 2087 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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