rs291107

Variant names:

• chr1-206901826-T-C
• rs291107
• NM_006850.3:c.463-172T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-206901826-T-C
• chr1-206901826-T-G

Variant summary

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

The NM_006850.3(IL24):​c.463-172T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 152,030 control chromosomes in the GnomAD database, including 24,801 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 (24801 hom., cov: 31)
• Consequence: IL24 NM_006850.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL24	NM_006850.3	c.463-172T>C		intron_variant	Intron 5 of 6	ENST00000294984.7	NP_006841.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL24	ENST00000294984.7	c.463-172T>C		intron_variant	Intron 5 of 6	1	NM_006850.3	ENSP00000294984.2

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83305 AN: 151912 Hom.: 24755 Cov.: 31

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.549 AC: 83413 AN: 152030 Hom.: 24801 Cov.: 31 AF XY: 0.537 AC XY: 39906 AN XY: 74300

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.568

Alfa AF: 0.495 Hom.: 25267

Bravo AF: 0.570

Asia WGS AF: 0.308 AC: 1071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.0
DANN	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs291107; hg19: chr1-207075171; COSMIC: COSV54321053; COSMIC: COSV54321053;