Variant rs2070874 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_000589.4(IL4):c.-33C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151898 control chromosomes in the gnomAD Genomes database, including 7661 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 0.28 ( 7661 hom., cov: 32)

Exomes 𝑓: 0.28 ( 14266 hom. )

Consequence

IL4
NM_000589.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.152

Links

IL4 (HGNC:6014):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BA1

GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
IL4	NM_000589.4 linkuse as main transcript	c.-33C>T	5_prime_UTR_variant	1/4	ENST00000231449.7
IL4	NM_001354990.2 linkuse as main transcript	c.-33C>T	5_prime_UTR_variant	1/5
IL4	NM_172348.3 linkuse as main transcript	c.-33C>T	5_prime_UTR_variant	1/3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL4	ENST00000231449.7 linkuse as main transcript	c.-33C>T	5_prime_UTR_variant	1/4	1	NM_000589.4	P1	P05112-1
IL4	ENST00000622422.1 linkuse as main transcript	c.-33C>T	5_prime_UTR_variant	1/5	1
IL4	ENST00000350025.2 linkuse as main transcript		upstream_gene_variant		1			P05112-2

Frequencies

GnomAD3 genomes

AF:

0.277

AC:

42143

AN:

151898

Hom.:

7661

Cov.:

show subpopulations

Gnomad AFR

AF:

0.416

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.310

Gnomad ASJ

AF:

0.229

Gnomad EAS

AF:

0.776

Gnomad SAS

AF:

0.192

Gnomad FIN

AF:

0.359

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.149

Gnomad OTH

AF:

0.240

GnomAD3 exomes

AF:

0.276

AC:

69369

AN:

250924

Hom.:

14266

AF XY:

0.255

AC XY:

34617

AN XY:

135604

show subpopulations

Gnomad AFR exome

AF:

0.423

Gnomad AMR exome

AF:

0.442

Gnomad ASJ exome

AF:

0.230

Gnomad EAS exome

AF:

0.792

Gnomad SAS exome

AF:

0.166

Gnomad FIN exome

AF:

0.351

Gnomad NFE exome

AF:

0.145

Gnomad OTH exome

AF:

0.217

GnomAD4 exome

AF:

0.180

AC:

260836

AN:

1450200

Hom.:

34991

AF XY:

0.177

AC XY:

127785

AN XY:

721696

show subpopulations

Gnomad4 AFR exome

AF:

0.416

Gnomad4 AMR exome

AF:

0.426

Gnomad4 ASJ exome

AF:

0.227

Gnomad4 EAS exome

AF:

0.736

Gnomad4 SAS exome

AF:

0.164

Gnomad4 FIN exome

AF:

0.343

Gnomad4 NFE exome

AF:

0.134

Gnomad4 OTH exome

AF:

0.210

Alfa

AF:

0.168

Hom.:

3121

Bravo

AF:

0.287

Asia WGS

AF:

0.462

AC:

1606

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

Cadd

Benign

7.2

Dann

Benign

0.82

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over