rs55699988

Variant names:

• chr16-3064391-G-C
• rs55699988
• ENST00000921321.1:c.-476G>C

Variant summary

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

The ENST00000921321.1(IL32):​c.-476G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,690 control chromosomes in the GnomAD database, including 13,303 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 0.41 (13303 hom., cov: 30)
• Consequence: IL32 ENST00000921321.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560
• Publications: 2 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 = 0.724 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000921321.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL32	ENST00000921321.1		c.-476G>C		5_prime_UTR	Exon 1 of 7	ENSP00000591380.1

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62305 AN: 151572 Hom.: 13302 Cov.: 30

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.411 AC: 62328 AN: 151690 Hom.: 13303 Cov.: 30 AF XY: 0.416 AC XY: 30807 AN XY: 74094

African (AFR) AF: 0.417 AC: 17237 AN: 41304

American (AMR) AF: 0.430 AC: 6561 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1454 AN: 3464

East Asian (EAS) AF: 0.744 AC: 3827 AN: 5144

South Asian (SAS) AF: 0.520 AC: 2495 AN: 4794

European-Finnish (FIN) AF: 0.341 AC: 3583 AN: 10514

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.378 AC: 25696 AN: 67904

Other (OTH) AF: 0.446 AC: 939 AN: 2106

Alfa AF: 0.370 Hom.: 1348

Bravo AF: 0.417

Asia WGS AF: 0.629 AC: 2186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.79
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs55699988; hg19: chr16-3114392;