16-3069086-C-A

Variant names:

• chr16-3069086-C-A
• NM_001376923.1:c.298C>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001376923.1(IL32):​c.298C>A​(p.Pro100Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 34)
• Consequence: IL32 NM_001376923.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.554

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08682406).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL32	NM_001376923.1	c.298C>A	p.Pro100Thr	missense_variant	Exon 7 of 7	ENST00000525643.7	NP_001363852.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL32	ENST00000525643.7	c.298C>A	p.Pro100Thr	missense_variant	Exon 7 of 7	1	NM_001376923.1	ENSP00000432218.3

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 53

GnomAD4 genome Cov.: 34

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jan 24, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.298C>A (p.P100T) alteration is located in exon 8 (coding exon 6) of the IL32 gene. This alteration results from a C to A substitution at nucleotide position 298, causing the proline (P) at amino acid position 100 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.079	T
BayesDel_noAF	Benign	-0.35
CADD	Benign	6.5
DANN	Uncertain	0.99
DEOGEN2	Benign	0.049	.;T;T;.;.;T;.;.;.;.;.;T;.;.;.;.;.;T;.;.;.;.;T;T;.;.;T;.;.
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.0040	N
LIST_S2	Benign	0.63	.;.;T;T;.;.;.;.;.;.;.;T;.;.;.;.;.;.;T;.;.;T;T;T;T;T;T;T;T
M_CAP	Benign	0.0062	T
MetaRNN	Benign	0.087	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	0.81	.;L;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;L;.;.;.;.;.;L;.;.;.;.;.
PrimateAI	Benign	0.42	T
PROVEAN	Uncertain	-4.2	D;D;.;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
REVEL	Benign	0.071
Sift	Benign	0.24	T;D;.;T;D;D;T;T;T;D;T;D;T;D;T;T;D;D;D;D;T;D;D;D;T;D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Polyphen		0.46	P;B;B;.;P;B;P;P;P;P;P;.;P;.;P;P;.;B;.;.;P;P;.;B;P;.;.;.;.
Vest4		0.28
MutPred		0.24		.;Gain of helix (P = 0.0093);.;.;.;.;.;.;.;.;.;Gain of helix (P = 0.0093);.;.;.;.;.;Gain of helix (P = 0.0093);.;.;.;.;.;Gain of helix (P = 0.0093);.;.;.;.;.;
MVP		0.31
MPC		0.56
ClinPred		0.26	T
GERP RS		-3.4
Varity_R		0.26
gMVP		0.010

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-3119087;