rs291109

Variant names:

• chr1-206898806-T-C
• rs291109
• NM_006850.3:c.45-514T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006850.3(IL24):​c.45-514T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,954 control chromosomes in the GnomAD database, including 24,731 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 0.55 (24731 hom., cov: 31)
• Consequence: IL24 NM_006850.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL24	NM_006850.3	c.45-514T>C		intron_variant	Intron 2 of 6	ENST00000294984.7	NP_006841.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL24	ENST00000294984.7	c.45-514T>C		intron_variant	Intron 2 of 6	1	NM_006850.3	ENSP00000294984.2

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83157 AN: 151836 Hom.: 24684 Cov.: 31

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.548 AC: 83266 AN: 151954 Hom.: 24731 Cov.: 31 AF XY: 0.537 AC XY: 39879 AN XY: 74288

African (AFR) AF: 0.782 AC: 32403 AN: 41444

American (AMR) AF: 0.515 AC: 7865 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1843 AN: 3464

East Asian (EAS) AF: 0.248 AC: 1279 AN: 5160

South Asian (SAS) AF: 0.254 AC: 1224 AN: 4816

European-Finnish (FIN) AF: 0.381 AC: 4021 AN: 10544

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32881 AN: 67928

Other (OTH) AF: 0.564 AC: 1191 AN: 2110

Alfa AF: 0.537 Hom.: 3323

Bravo AF: 0.570

Asia WGS AF: 0.308 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.013
DANN	Benign	0.34
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs291109; hg19: chr1-207072151;