16-3066169-A-G

Variant names:

• chr16-3066169-A-G
• rs11860424
• NM_001376923.1:c.15+343A>G

Variant summary

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

The NM_001376923.1(IL32):​c.15+343A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,934 control chromosomes in the GnomAD database, including 22,004 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 0.53 (22004 hom., cov: 32)
• Consequence: IL32 NM_001376923.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL32	NM_001376923.1	c.15+343A>G		intron_variant	Intron 2 of 6	ENST00000525643.7	NP_001363852.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL32	ENST00000525643.7	c.15+343A>G		intron_variant	Intron 2 of 6	1	NM_001376923.1	ENSP00000432218.3

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80849 AN: 151816 Hom.: 21970 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.533 AC: 80932 AN: 151934 Hom.: 22004 Cov.: 32 AF XY: 0.538 AC XY: 39976 AN XY: 74268

African (AFR) AF: 0.607 AC: 25160 AN: 41424

American (AMR) AF: 0.589 AC: 8997 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1564 AN: 3470

East Asian (EAS) AF: 0.655 AC: 3366 AN: 5140

South Asian (SAS) AF: 0.562 AC: 2701 AN: 4810

European-Finnish (FIN) AF: 0.527 AC: 5566 AN: 10568

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31898 AN: 67930

Other (OTH) AF: 0.518 AC: 1090 AN: 2104

Alfa AF: 0.499 Hom.: 30952

Bravo AF: 0.542

Asia WGS AF: 0.650 AC: 2254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.5
DANN	Benign	0.39
PhyloP100		-0.37
PromoterAI		-0.039	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs11860424; hg19: chr16-3116170;