Variant 5-132660151-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002188.3(IL13):c.334-24T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 1,609,364 control chromosomes in the GnomAD database, including 471,012 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 0.63 ( 33058 hom., cov: 32)

Exomes 𝑓: 0.77 ( 437954 hom. )

Consequence

IL13
NM_002188.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.729

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
IL13	NM_002188.3 linkuse as main transcript	c.334-24T>C	intron_variant	ENST00000304506.7	NP_002179.2
IL13	NM_001354991.2 linkuse as main transcript	c.139-24T>C	intron_variant		NP_001341920.1
IL13	NM_001354992.2 linkuse as main transcript	c.139-24T>C	intron_variant		NP_001341921.1
IL13	NM_001354993.2 linkuse as main transcript	c.139-24T>C	intron_variant		NP_001341922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL13	ENST00000304506.7 linkuse as main transcript	c.334-24T>C		intron_variant		1	NM_002188.3	ENSP00000304915	P1
TH2LCRR	ENST00000435042.1 linkuse as main transcript	n.94+4028A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.631

AC:

95834

AN:

151944

Hom.:

33064

Cov.:

show subpopulations

Gnomad AFR

AF:

0.348

Gnomad AMI

AF:

0.874

Gnomad AMR

AF:

0.606

Gnomad ASJ

AF:

0.731

Gnomad EAS

AF:

0.673

Gnomad SAS

AF:

0.692

Gnomad FIN

AF:

0.611

Gnomad MID

AF:

0.712

Gnomad NFE

AF:

0.794

Gnomad OTH

AF:

0.677

GnomAD3 exomes

AF:

0.679

AC:

169794

AN:

250072

Hom.:

60788

AF XY:

0.698

AC XY:

94378

AN XY:

135280

show subpopulations

Gnomad AFR exome

AF:

0.339

Gnomad AMR exome

AF:

0.439

Gnomad ASJ exome

AF:

0.741

Gnomad EAS exome

AF:

0.673

Gnomad SAS exome

AF:

0.690

Gnomad FIN exome

AF:

0.624

Gnomad NFE exome

AF:

0.801

Gnomad OTH exome

AF:

0.728

GnomAD4 exome

AF:

0.768

AC:

1118945

AN:

1457302

Hom.:

437954

Cov.:

AF XY:

0.768

AC XY:

556806

AN XY:

725290

show subpopulations

Gnomad4 AFR exome

AF:

0.338

Gnomad4 AMR exome

AF:

0.461

Gnomad4 ASJ exome

AF:

0.742

Gnomad4 EAS exome

AF:

0.683

Gnomad4 SAS exome

AF:

0.690

Gnomad4 FIN exome

AF:

0.628

Gnomad4 NFE exome

AF:

0.811

Gnomad4 OTH exome

AF:

0.744

GnomAD4 genome

AF:

0.630

AC:

95842

AN:

152062

Hom.:

33058

Cov.:

AF XY:

0.624

AC XY:

46356

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.347

Gnomad4 AMR

AF:

0.606

Gnomad4 ASJ

AF:

0.731

Gnomad4 EAS

AF:

0.672

Gnomad4 SAS

AF:

0.692

Gnomad4 FIN

AF:

0.611

Gnomad4 NFE

AF:

0.794

Gnomad4 OTH

AF:

0.679

Alfa

AF:

0.763

Hom.:

79494

Bravo

AF:

0.614

Asia WGS

AF:

0.650

AC:

2261

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.61

DANN

Benign

0.21

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over