dbSNP rs2239303: IL32:c.115-48G>A (chr16-3067936-G-A) – 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.115-48G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 1,605,396 control chromosomes in the GnomAD database, including 326,550 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 0.62 ( 29443 hom., cov: 32)

Exomes 𝑓: 0.64 ( 297107 hom. )

Consequence

IL32
NM_001376923.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.54

Publications

14 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=-1.02).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001376923.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IL32	NM_001376923.1	MANE Select	c.115-48G>A	intron	N/A	NP_001363852.1	P24001-2
IL32	NM_001308078.4		c.253-48G>A	intron	N/A	NP_001295007.1	P24001-1
IL32	NM_001369587.3		c.253-48G>A	intron	N/A	NP_001356516.1	P24001-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IL32	ENST00000525643.7	TSL:1 MANE Select	c.115-48G>A	intron	N/A	ENSP00000432218.3	P24001-2
IL32	ENST00000396890.6	TSL:1	c.253-48G>A	intron	N/A	ENSP00000380099.2	P24001-1
IL32	ENST00000325568.9	TSL:1	c.115-48G>A	intron	N/A	ENSP00000324742.5	P24001-2

Frequencies

GnomAD3 genomes

AF:

0.620

AC:

94234

AN:

151908

Hom.:

29419

Cov.:

show subpopulations

Gnomad AFR

AF:

0.588

Gnomad AMI

AF:

0.748

Gnomad AMR

AF:

0.550

Gnomad ASJ

AF:

0.678

Gnomad EAS

AF:

0.481

Gnomad SAS

AF:

0.565

Gnomad FIN

AF:

0.679

Gnomad MID

AF:

0.554

Gnomad NFE

AF:

0.657

Gnomad OTH

AF:

0.621

GnomAD2 exomes

AF:

0.602

AC:

150810

AN:

250540

AF XY:

0.607

show subpopulations

Gnomad AFR exome

AF:

0.587

Gnomad AMR exome

AF:

0.471

Gnomad ASJ exome

AF:

0.674

Gnomad EAS exome

AF:

0.455

Gnomad FIN exome

AF:

0.674

Gnomad NFE exome

AF:

0.657

Gnomad OTH exome

AF:

0.613

GnomAD4 exome

AF:

0.637

AC:

925819

AN:

1453368

Hom.:

297107

Cov.:

AF XY:

0.636

AC XY:

460153

AN XY:

723586

show subpopulations

African (AFR)

AF:

0.588

AC:

19575

AN:

33302

American (AMR)

AF:

0.482

AC:

21515

AN:

44664

Ashkenazi Jewish (ASJ)

AF:

0.676

AC:

17630

AN:

26080

East Asian (EAS)

AF:

0.528

AC:

20950

AN:

39650

South Asian (SAS)

AF:

0.560

AC:

48169

AN:

86056

European-Finnish (FIN)

AF:

0.670

AC:

35799

AN:

53394

Middle Eastern (MID)

AF:

0.592

AC:

3406

AN:

5752

European-Non Finnish (NFE)

AF:

0.653

AC:

721117

AN:

1104390

Other (OTH)

AF:

0.627

AC:

37658

AN:

60080

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

18064

36128

54192

72256

90320

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18704

37408

56112

74816

93520

<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:

0.620

AC:

94313

AN:

152028

Hom.:

29443

Cov.:

AF XY:

0.620

AC XY:

46051

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.588

AC:

24365

AN:

41448

American (AMR)

AF:

0.549

AC:

8407

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.678

AC:

2355

AN:

3472

East Asian (EAS)

AF:

0.482

AC:

2489

AN:

5166

South Asian (SAS)

AF:

0.564

AC:

2721

AN:

4826

European-Finnish (FIN)

AF:

0.679

AC:

7180

AN:

10580

Middle Eastern (MID)

AF:

0.561

AC:

165

AN:

294

European-Non Finnish (NFE)

AF:

0.657

AC:

44639

AN:

67922

Other (OTH)

AF:

0.622

AC:

1313

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1845

3689

5534

7378

9223

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

776

1552

2328

3104

3880

<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:

0.637

Hom.:

45836

Bravo

AF:

0.610

Asia WGS

AF:

0.531

AC:

1848

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.32

(source)

DANN

Benign

0.37

PhyloP100

-1.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over