Variant rs1124053 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_022789.4(IL25):c.424C>A(p.Arg142=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 1,614,028 control chromosomes in the GnomAD database, including 41,201 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 0.25 ( 5461 hom., cov: 33)

Exomes 𝑓: 0.22 ( 35740 hom. )

Consequence

IL25
NM_022789.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.869

Variant links:

Genes affected

IL25 (HGNC:13765): (interleukin 25) The protein encoded by this gene is a cytokine that shares sequence similarity with interleukin 17. This cytokine can induce NF-kappaB activation, and stimulate the production of interleukin 8. Both this cytokine and interleukin 17B are ligands for the cytokine receptor IL17BR. Studies of a similar gene in mice suggest that this cytokine may be a pro-inflammatory cytokine favoring the Th2-type immune response. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]

IL25 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.25).

BP7

Synonymous conserved (PhyloP=0.869 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL25	NM_172314.2 linkuse as main transcript	c.376C>A	p.Arg126=	synonymous_variant	3/3	ENST00000397242.3	NP_758525.1
IL25	NM_022789.4 linkuse as main transcript	c.424C>A	p.Arg142=	synonymous_variant	2/2		NP_073626.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL25	ENST00000397242.3 linkuse as main transcript	c.376C>A	p.Arg126=	synonymous_variant	3/3	1	NM_172314.2	ENSP00000380417	P2	Q9H293-2
IL25	ENST00000329715.2 linkuse as main transcript	c.424C>A	p.Arg142=	synonymous_variant	2/2	1		ENSP00000328111	A2	Q9H293-1

Frequencies

GnomAD3 genomes

AF:

0.254

AC:

38555

AN:

152038

Hom.:

5444

Cov.:

show subpopulations

Gnomad AFR

AF:

0.376

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.198

Gnomad ASJ

AF:

0.191

Gnomad EAS

AF:

0.255

Gnomad SAS

AF:

0.203

Gnomad FIN

AF:

0.189

Gnomad MID

AF:

0.258

Gnomad NFE

AF:

0.209

Gnomad OTH

AF:

0.265

GnomAD3 exomes

AF:

0.210

AC:

52860

AN:

251366

Hom.:

6045

AF XY:

0.209

AC XY:

28460

AN XY:

135878

show subpopulations

Gnomad AFR exome

AF:

0.380

Gnomad AMR exome

AF:

0.144

Gnomad ASJ exome

AF:

0.192

Gnomad EAS exome

AF:

0.261

Gnomad SAS exome

AF:

0.204

Gnomad FIN exome

AF:

0.177

Gnomad NFE exome

AF:

0.208

Gnomad OTH exome

AF:

0.213

GnomAD4 exome

AF:

0.217

AC:

317570

AN:

1461874

Hom.:

35740

Cov.:

AF XY:

0.216

AC XY:

156888

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.383

Gnomad4 AMR exome

AF:

0.152

Gnomad4 ASJ exome

AF:

0.193

Gnomad4 EAS exome

AF:

0.255

Gnomad4 SAS exome

AF:

0.203

Gnomad4 FIN exome

AF:

0.178

Gnomad4 NFE exome

AF:

0.217

Gnomad4 OTH exome

AF:

0.230

GnomAD4 genome

AF:

0.254

AC:

38607

AN:

152154

Hom.:

5461

Cov.:

AF XY:

0.250

AC XY:

18602

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.376

Gnomad4 AMR

AF:

0.197

Gnomad4 ASJ

AF:

0.191

Gnomad4 EAS

AF:

0.255

Gnomad4 SAS

AF:

0.204

Gnomad4 FIN

AF:

0.189

Gnomad4 NFE

AF:

0.209

Gnomad4 OTH

AF:

0.273

Alfa

AF:

0.177

Hom.:

809

Bravo

AF:

0.262

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.25

CADD

Benign

9.6

DANN

Benign

0.74

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

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