rs1150256

Positions:

• chr1-206899788-G-A
• chr1-206899788-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006850.3(IL24):​c.240+273G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 151,864 control chromosomes in the GnomAD database, including 12,527 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 0.40 (12527 hom., cov: 31)
• Consequence: IL24 NM_006850.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL24	NM_006850.3	c.240+273G>A		intron_variant		ENST00000294984.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL24	ENST00000294984.7	c.240+273G>A		intron_variant		1	NM_006850.3	P4

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60246 AN: 151746 Hom.: 12522 Cov.: 31

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.440

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.397 AC: 60289 AN: 151864 Hom.: 12527 Cov.: 31 AF XY: 0.391 AC XY: 29003 AN XY: 74206

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.441

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: 0.444

Alfa AF: 0.431 Hom.: 2125

Bravo AF: 0.399

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.79

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

Other links and lift over

dbSNP: rs1150256; hg19: chr1-207073133;