16-3067606-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001376923.1(IL32):c.107G>A(p.Arg36His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00389 in 1,610,386 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R36C) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0039 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0039 ( 20 hom. )

Consequence

IL32
NM_001376923.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.07

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0044682026).

BP6

Variant 16-3067606-G-A is Benign according to our data. Variant chr16-3067606-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 710339.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL32	NM_001376923.1 linkuse as main transcript	c.107G>A	p.Arg36His	missense_variant	4/7	ENST00000525643.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL32	ENST00000525643.7 linkuse as main transcript	c.107G>A	p.Arg36His	missense_variant	4/7	1	NM_001376923.1	A2	P24001-2

Frequencies

GnomAD3 genomes

AF:

0.00393

AC:

598

AN:

152146

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00217

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00118

Gnomad ASJ

AF:

0.00461

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.00772

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00565

Gnomad OTH

AF:

0.000957

GnomAD3 exomes

AF:

0.00371

AC:

928

AN:

250216

Hom.:

AF XY:

0.00382

AC XY:

517

AN XY:

135330

show subpopulations

Gnomad AFR exome

AF:

0.00209

Gnomad AMR exome

AF:

0.000811

Gnomad ASJ exome

AF:

0.00398

Gnomad EAS exome

AF:

0.000218

Gnomad SAS exome

AF:

0.00134

Gnomad FIN exome

AF:

0.00765

Gnomad NFE exome

AF:

0.00528

Gnomad OTH exome

AF:

0.00376

GnomAD4 exome

AF:

0.00389

AC:

5672

AN:

1458122

Hom.:

Cov.:

AF XY:

0.00390

AC XY:

2829

AN XY:

725620

show subpopulations

Gnomad4 AFR exome

AF:

0.00180

Gnomad4 AMR exome

AF:

0.000850

Gnomad4 ASJ exome

AF:

0.00433

Gnomad4 EAS exome

AF:

0.000227

Gnomad4 SAS exome

AF:

0.00151

Gnomad4 FIN exome

AF:

0.00818

Gnomad4 NFE exome

AF:

0.00425

Gnomad4 OTH exome

AF:

0.00272

GnomAD4 genome

AF:

0.00393

AC:

598

AN:

152264

Hom.:

Cov.:

AF XY:

0.00400

AC XY:

298

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00217

Gnomad4 AMR

AF:

0.00118

Gnomad4 ASJ

AF:

0.00461

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00103

Gnomad4 FIN

AF:

0.00772

Gnomad4 NFE

AF:

0.00565

Gnomad4 OTH

AF:

0.000947

Alfa

AF:

0.00435

Hom.:

Bravo

AF:

0.00294

TwinsUK

AF:

0.00243

AC:

ALSPAC

AF:

0.00285

AC:

ESP6500AA

AF:

0.00205

AC:

ESP6500EA

AF:

0.00360

AC:

ExAC

AF:

0.00414

AC:

503

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00289

EpiControl

AF:

0.00332

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Jul 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.094

BayesDel_addAF

Benign

-0.43

BayesDel_noAF

Benign

-0.38

Cadd

Benign

1.1

Dann

Benign

0.96

Eigen

Benign

-1.9

Eigen_PC

Benign

-1.9

FATHMM_MKL

Benign

0.0016

M_CAP

Benign

0.016

MetaRNN

Benign

0.0045

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

-0.99

MutationTaster

Benign

1.0

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

PrimateAI

Benign

0.36

PROVEAN

Benign

-1.0

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

0.089

Sift

Benign

0.087

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

Sift4G

Benign

0.19

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

Polyphen

0.0020

B;B;B;.;B;B;B;B;B;B;B;B;B;B;B;B;.;B;B;B;.;B;B;.;.

Vest4

0.12

MVP

0.40

MPC

0.15

ClinPred

0.0035

GERP RS

-4.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.061

gMVP

0.0075

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over