dbSNP rs28372698: IL32:c.-413T>A (chr16-3065110-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000325568.9(IL32):c.-413T>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,086 control chromosomes in the GnomAD database, including 11,696 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 0.38 ( 11696 hom., cov: 34)

Consequence

IL32
ENST00000325568.9 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.603

Variant links:

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]

IL32 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein	UniProt
IL32	ENST00000325568.9 link	c.-413T>A	upstream_gene_variant	1	ENSP00000324742.5	P24001-2
IL32	ENST00000531965.5 link	c.-400T>A	upstream_gene_variant	1	ENSP00000433177.1	P24001-3
IL32	ENST00000529699.5 link	c.-413T>A	upstream_gene_variant	1	ENSP00000436937.1	C6GKH1

Frequencies

GnomAD3 genomes

AF:

0.384

AC:

58382

AN:

151968

Hom.:

11693

Cov.:

show subpopulations

Gnomad AFR

AF:

0.302

Gnomad AMI

AF:

0.433

Gnomad AMR

AF:

0.417

Gnomad ASJ

AF:

0.415

Gnomad EAS

AF:

0.688

Gnomad SAS

AF:

0.508

Gnomad FIN

AF:

0.381

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.392

Gnomad OTH

AF:

0.403

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

GnomAD4 genome

AF:

0.384

AC:

58408

AN:

152086

Hom.:

11696

Cov.:

AF XY:

0.390

AC XY:

29011

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.302

Gnomad4 AMR

AF:

0.417

Gnomad4 ASJ

AF:

0.415

Gnomad4 EAS

AF:

0.690

Gnomad4 SAS

AF:

0.506

Gnomad4 FIN

AF:

0.381

Gnomad4 NFE

AF:

0.392

Gnomad4 OTH

AF:

0.407

Alfa

AF:

0.208

Hom.:

442

Bravo

AF:

0.381

Asia WGS

AF:

0.596

AC:

2071

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.78

DANN

Benign

0.56

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over