Genetic Variant IL32:c.202-126T>C (chr16-3068864-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001376923.1(IL32):c.202-126T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 1,461,746 control chromosomes in the GnomAD database, including 256,348 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 0.57 ( 24871 hom., cov: 32)

Exomes 𝑓: 0.59 ( 231477 hom. )

Consequence

IL32
NM_001376923.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.901

Publications

16 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL32	NM_001376923.1 link	c.202-126T>C		intron_variant	Intron 6 of 6	ENST00000525643.7	NP_001363852.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL32	ENST00000525643.7 link	c.202-126T>C		intron_variant	Intron 6 of 6	1	NM_001376923.1	ENSP00000432218.3		P24001-2

Frequencies

GnomAD3 genomes

AF:

0.569

AC:

86416

AN:

151770

Hom.:

24857

Cov.:

show subpopulations

Gnomad AFR

AF:

0.526

Gnomad AMI

AF:

0.770

Gnomad AMR

AF:

0.523

Gnomad ASJ

AF:

0.605

Gnomad EAS

AF:

0.420

Gnomad SAS

AF:

0.597

Gnomad FIN

AF:

0.574

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.610

Gnomad OTH

AF:

0.580

GnomAD4 exome

AF:

0.593

AC:

776633

AN:

1309858

Hom.:

231477

AF XY:

0.594

AC XY:

381466

AN XY:

642706

show subpopulations

African (AFR)

AF:

0.520

AC:

14935

AN:

28730

American (AMR)

AF:

0.457

AC:

12045

AN:

26362

Ashkenazi Jewish (ASJ)

AF:

0.602

AC:

11945

AN:

19852

East Asian (EAS)

AF:

0.456

AC:

16826

AN:

36862

South Asian (SAS)

AF:

0.601

AC:

40833

AN:

67924

European-Finnish (FIN)

AF:

0.573

AC:

26795

AN:

46722

Middle Eastern (MID)

AF:

0.541

AC:

2336

AN:

4318

European-Non Finnish (NFE)

AF:

0.604

AC:

619426

AN:

1024860

Other (OTH)

AF:

0.581

AC:

31492

AN:

54228

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

15952

31904

47856

63808

79760

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17148

34296

51444

68592

85740

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.569

AC:

86488

AN:

151888

Hom.:

24871

Cov.:

AF XY:

0.567

AC XY:

42108

AN XY:

74248

show subpopulations

African (AFR)

AF:

0.526

AC:

21787

AN:

41404

American (AMR)

AF:

0.523

AC:

7991

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.605

AC:

2101

AN:

3472

East Asian (EAS)

AF:

0.421

AC:

2166

AN:

5146

South Asian (SAS)

AF:

0.596

AC:

2862

AN:

4802

European-Finnish (FIN)

AF:

0.574

AC:

6077

AN:

10582

Middle Eastern (MID)

AF:

0.544

AC:

160

AN:

294

European-Non Finnish (NFE)

AF:

0.610

AC:

41416

AN:

67904

Other (OTH)

AF:

0.583

AC:

1229

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1882

3763

5645

7526

9408

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

738

1476

2214

2952

3690

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.589

Hom.:

4067

Bravo

AF:

0.561

Asia WGS

AF:

0.514

AC:

1790

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.39

(source)

DANN

Benign

0.47

PhyloP100

-0.90

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over