dbSNP rs2069739: IL13:c.-93+286A>G (chr5-132656916-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001354991.2(IL13):c.-93+286A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0936 in 152,512 control chromosomes in the GnomAD database, including 1,738 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 0.094 ( 1737 hom., cov: 32)

Exomes 𝑓: 0.035 ( 1 hom. )

Consequence

IL13
NM_001354991.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.723

Publications

6 publications found

Variant links:

Genes affected

IL13 (HGNC:5973): (interleukin 13) This gene encodes an immunoregulatory cytokine produced primarily by activated Th2 cells. This cytokine is involved in several stages of B-cell maturation and differentiation. It up-regulates CD23 and MHC class II expression, and promotes IgE isotype switching of B cells. This cytokine down-regulates macrophage activity, thereby inhibits the production of pro-inflammatory cytokines and chemokines. This cytokine is found to be critical to the pathogenesis of allergen-induced asthma but operates through mechanisms independent of IgE and eosinophils. This gene, IL3, IL5, IL4, and CSF2 form a cytokine gene cluster on chromosome 5q, with this gene particularly close to IL4. [provided by RefSeq, Jul 2008]

IL13 links:

TH2LCRR (HGNC:40495): (T helper type 2 locus control region associated RNA)

TH2LCRR 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 = 0.279 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001354991.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
IL13	NM_001354991.2	c.-93+286A>G	intron	N/A	NP_001341920.1	Q4VB53
IL13	NM_001354992.2	c.-271-150A>G	intron	N/A	NP_001341921.1	Q4VB53
IL13	NM_001354993.2	c.-200-150A>G	intron	N/A	NP_001341922.1	Q4VB53

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
TH2LCRR	ENST00000435042.1	TSL:5	n.94+7263T>C	intron	N/A
IL13	ENST00000459878.5	TSL:3	n.107+286A>G	intron	N/A
IL13	ENST00000468334.5	TSL:3	n.369-150A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0935

AC:

14216

AN:

152054

Hom.:

1733

Cov.:

show subpopulations

Gnomad AFR

AF:

0.283

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0454

Gnomad ASJ

AF:

0.0397

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0409

Gnomad FIN

AF:

0.00697

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0183

Gnomad OTH

AF:

0.0740

GnomAD4 exome

AF:

0.0353

AC:

AN:

340

Hom.:

AF XY:

0.0313

AC XY:

AN XY:

224

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.0333

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0194

AC:

AN:

258

Other (OTH)

AF:

0.150

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.530

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0937

AC:

14261

AN:

152172

Hom.:

1737

Cov.:

AF XY:

0.0916

AC XY:

6815

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.283

AC:

11741

AN:

41476

American (AMR)

AF:

0.0453

AC:

693

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0397

AC:

138

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5178

South Asian (SAS)

AF:

0.0412

AC:

198

AN:

4808

European-Finnish (FIN)

AF:

0.00697

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0183

AC:

1242

AN:

68010

Other (OTH)

AF:

0.0732

AC:

154

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

560

1120

1680

2240

2800

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

264

396

528

660

<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:

0.0359

Hom.:

593

Bravo

AF:

0.106

Asia WGS

AF:

0.0370

AC:

129

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.4

(source)

DANN

Benign

0.25

PhyloP100

-0.72

Splicing

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