dbSNP rs2069882: IL9:c.315+76A>G (chr5-135893944-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_000590.2(IL9):c.315+76A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 1,245,016 control chromosomes in the GnomAD database, including 27,734 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 0.24 ( 4698 hom., cov: 32)

Exomes 𝑓: 0.20 ( 23036 hom. )

Consequence

IL9
NM_000590.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0660

Publications

15 publications found

Variant links:

Genes affected

IL9 (HGNC:6029): (interleukin 9) The protein encoded by this gene is a cytokine that acts as a regulator of a variety of hematopoietic cells. This cytokine stimulates cell proliferation and prevents apoptosis. It functions through the interleukin 9 receptor (IL9R), which activates different signal transducer and activator (STAT) proteins and thus connects this cytokine to various biological processes. The gene encoding this cytokine has been identified as a candidate gene for asthma. Genetic studies on a mouse model of asthma demonstrated that this cytokine is a determining factor in the pathogenesis of bronchial hyperresponsiveness. [provided by RefSeq, Jul 2008]

IL9 links:

LOC124901074 (HGNC:):

LOC124901074 links:

Genome browser will be placed here

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL9	NM_000590.2 link	c.315+76A>G		intron_variant	Intron 4 of 4	ENST00000274520.2	NP_000581.1
LOC124901074	XR_007058947.1 link	n.508+1341T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL9	ENST00000274520.2 link	c.315+76A>G		intron_variant	Intron 4 of 4	1	NM_000590.2	ENSP00000274520.1

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35752

AN:

152044

Hom.:

4683

Cov.:

show subpopulations

Gnomad AFR

AF:

0.349

Gnomad AMI

AF:

0.272

Gnomad AMR

AF:

0.172

Gnomad ASJ

AF:

0.345

Gnomad EAS

AF:

0.0386

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.185

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.235

GnomAD4 exome

AF:

0.198

AC:

215864

AN:

1092854

Hom.:

23036

AF XY:

0.197

AC XY:

107984

AN XY:

548140

show subpopulations

African (AFR)

AF:

0.358

AC:

8674

AN:

24236

American (AMR)

AF:

0.118

AC:

2697

AN:

22928

Ashkenazi Jewish (ASJ)

AF:

0.345

AC:

6625

AN:

19214

East Asian (EAS)

AF:

0.0618

AC:

2201

AN:

35610

South Asian (SAS)

AF:

0.158

AC:

9783

AN:

61784

European-Finnish (FIN)

AF:

0.194

AC:

9479

AN:

48840

Middle Eastern (MID)

AF:

0.262

AC:

1050

AN:

4014

European-Non Finnish (NFE)

AF:

0.200

AC:

165520

AN:

829270

Other (OTH)

AF:

0.209

AC:

9835

AN:

46958

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

8225

16450

24674

32899

41124

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5348

10696

16044

21392

26740

<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:

0.235

AC:

35802

AN:

152162

Hom.:

4698

Cov.:

AF XY:

0.232

AC XY:

17238

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.350

AC:

14504

AN:

41476

American (AMR)

AF:

0.172

AC:

2625

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.345

AC:

1197

AN:

3470

East Asian (EAS)

AF:

0.0387

AC:

201

AN:

5190

South Asian (SAS)

AF:

0.153

AC:

736

AN:

4822

European-Finnish (FIN)

AF:

0.185

AC:

1963

AN:

10590

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.202

AC:

13766

AN:

68000

Other (OTH)

AF:

0.233

AC:

493

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1379

2757

4136

5514

6893

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

362

724

1086

1448

1810

<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:

0.210

Hom.:

2646

Bravo

AF:

0.238

Asia WGS

AF:

0.126

AC:

442

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.8

(source)

DANN

Benign

0.25

PhyloP100

-0.066

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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