Variant 16-3067377-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001376923.1(IL32):c.16G>T(p.Val6Phe) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,386,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 18/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.000014 ( 0 hom. )

Consequence

IL32
NM_001376923.1 missense, splice_region

Scores

Splicing: ADA: 0.005674

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.43

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 Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.058654666).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL32	NM_001376923.1 link	c.16G>T	p.Val6Phe	missense_variant, splice_region_variant	Exon 3 of 7	ENST00000525643.7	NP_001363852.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL32	ENST00000525643.7 link	c.16G>T	p.Val6Phe	missense_variant, splice_region_variant	Exon 3 of 7	1	NM_001376923.1	ENSP00000432218.3		P24001-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000509

AC:

AN:

196390

Hom.:

AF XY:

0.00000958

AC XY:

AN XY:

104342

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000107

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000137

AC:

AN:

1386994

Hom.:

Cov.:

AF XY:

0.0000132

AC XY:

AN XY:

683060

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000158

Gnomad4 OTH exome

AF:

0.0000350

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.083

BayesDel_noAF

Benign

-0.36

CADD

Benign

1.3

DANN

Benign

0.96

DEOGEN2

Benign

0.017

.;T;T;.;T;.;.;.;.;.;T;.;.;.;.;.;T;.;.;.;.;.;T;.;.;T;.;.

Eigen

Benign

-1.8

Eigen_PC

Benign

-1.9

FATHMM_MKL

Benign

0.0022

LIST_S2

Benign

0.41

.;.;T;.;.;.;.;.;.;.;T;.;.;.;.;.;.;T;.;T;.;T;T;T;T;T;T;T

M_CAP

Benign

0.038

MetaRNN

Benign

0.059

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

-0.97

MutationAssessor

Benign

0.0

N;N;.;N;.;N;N;N;N;N;.;N;N;N;N;N;N;.;N;.;N;N;N;N;N;.;N;N

PrimateAI

Benign

0.46

PROVEAN

Benign

-1.2

N;N;.;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N

REVEL

Benign

0.080

Sift

Benign

0.17

T;D;.;D;T;T;T;T;D;T;D;T;T;T;T;T;D;D;T;D;T;D;D;T;T;D;T;D

Sift4G

Benign

0.25

.;T;D;.;D;.;.;.;.;.;T;.;D;.;.;D;T;D;D;T;.;.;T;.;D;T;D;D

Polyphen

0.39

B;B;B;B;B;B;B;B;B;B;P;B;.;B;B;.;B;.;.;P;B;B;B;B;.;.;.;.

Vest4

0.14

MutPred

0.23

Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);Loss of MoRF binding (P = 0.0753);

MVP

0.29

MPC

0.52

ClinPred

0.071

GERP RS

-3.8

Varity_R

0.19

gMVP

0.0054

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0057

dbscSNV1_RF

Benign

0.20

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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