Variant 1-206899614-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_006850.3(IL24):c.240+99C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 981,556 control chromosomes in the GnomAD database, including 94,226 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.39 ( 12369 hom., cov: 32)

Exomes 𝑓: 0.44 ( 81857 hom. )

Consequence

IL24
NM_006850.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.350

Variant links:

Genes affected

IL24 (HGNC:11346): (interleukin 24) This gene encodes a member of the IL10 family of cytokines. It was identified as a gene induced during terminal differentiation in melanoma cells. The protein encoded by this gene can induce apoptosis selectively in various cancer cells. Overexpression of this gene leads to elevated expression of several GADD family genes, which correlates with the induction of apoptosis. The phosphorylation of mitogen-activated protein kinase 14 (MAPK7/P38), and heat shock 27kDa protein 1 (HSPB2/HSP27) are found to be induced by this gene in melanoma cells, but not in normal immortal melanocytes. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

IL24 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 1-206899614-C-T is Benign according to our data. Variant chr1-206899614-C-T is described in ClinVar as [Benign]. Clinvar id is 2688458.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL24	NM_006850.3 linkuse as main transcript	c.240+99C>T		intron_variant		ENST00000294984.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL24	ENST00000294984.7 linkuse as main transcript	c.240+99C>T		intron_variant		1	NM_006850.3	P4	Q13007-1

Frequencies

GnomAD3 genomes

AF:

0.394

AC:

59819

AN:

151936

Hom.:

12364

Cov.:

show subpopulations

Gnomad AFR

AF:

0.290

Gnomad AMI

AF:

0.433

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.472

Gnomad EAS

AF:

0.226

Gnomad SAS

AF:

0.239

Gnomad FIN

AF:

0.378

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.467

Gnomad OTH

AF:

0.437

GnomAD4 exome

AF:

0.438

AC:

363428

AN:

829502

Hom.:

81857

AF XY:

0.434

AC XY:

181016

AN XY:

417446

show subpopulations

Gnomad4 AFR exome

AF:

0.287

Gnomad4 AMR exome

AF:

0.460

Gnomad4 ASJ exome

AF:

0.487

Gnomad4 EAS exome

AF:

0.255

Gnomad4 SAS exome

AF:

0.253

Gnomad4 FIN exome

AF:

0.390

Gnomad4 NFE exome

AF:

0.469

Gnomad4 OTH exome

AF:

0.428

GnomAD4 genome

AF:

0.394

AC:

59863

AN:

152054

Hom.:

12369

Cov.:

AF XY:

0.388

AC XY:

28793

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.290

Gnomad4 AMR

AF:

0.439

Gnomad4 ASJ

AF:

0.472

Gnomad4 EAS

AF:

0.225

Gnomad4 SAS

AF:

0.239

Gnomad4 FIN

AF:

0.378

Gnomad4 NFE

AF:

0.467

Gnomad4 OTH

AF:

0.441

Alfa

AF:

0.461

Hom.:

16074

Bravo

AF:

0.395

Asia WGS

AF:

0.256

AC:

890

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 31% of patients studied by a panel of primary immunodeficiencies. Number of patients: 27. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.1

DANN

Benign

0.67

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

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over