rs1150255

Variant names:

• chr1-206899614-C-T
• rs1150255
• NM_006850.3:c.240+99C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.350
• Publications: 11 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 -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006850.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL24	NM_006850.3	MANE Select	c.240+99C>T		intron	N/A	NP_006841.1	Q13007-1
	IL24	NM_001185156.1		c.243+99C>T		intron	N/A	NP_001172085.1	Q13007-2
	IL24	NM_001185157.1		c.243+99C>T		intron	N/A	NP_001172086.1	Q13007-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL24	ENST00000294984.7	TSL:1 MANE Select	c.240+99C>T		intron	N/A	ENSP00000294984.2	Q13007-1
	IL24	ENST00000391929.7	TSL:1	c.243+99C>T		intron	N/A	ENSP00000375795.3	Q13007-2
	IL24	ENST00000367093.3	TSL:1	c.243+99C>T		intron	N/A	ENSP00000356060.3	Q13007-3

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59819 AN: 151936 Hom.: 12364 Cov.: 32

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

African (AFR) AF: 0.287 AC: 5630 AN: 19642

American (AMR) AF: 0.460 AC: 10022 AN: 21782

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 7541 AN: 15474

East Asian (EAS) AF: 0.255 AC: 8541 AN: 33534

South Asian (SAS) AF: 0.253 AC: 12180 AN: 48144

European-Finnish (FIN) AF: 0.390 AC: 13949 AN: 35746

Middle Eastern (MID) AF: 0.487 AC: 1570 AN: 3222

European-Non Finnish (NFE) AF: 0.469 AC: 287751 AN: 614002

Other (OTH) AF: 0.428 AC: 16244 AN: 37956

GnomAD4 genome AF: 0.394 AC: 59863 AN: 152054 Hom.: 12369 Cov.: 32 AF XY: 0.388 AC XY: 28793 AN XY: 74302

African (AFR) AF: 0.290 AC: 12024 AN: 41486

American (AMR) AF: 0.439 AC: 6707 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1636 AN: 3468

East Asian (EAS) AF: 0.225 AC: 1164 AN: 5172

South Asian (SAS) AF: 0.239 AC: 1154 AN: 4824

European-Finnish (FIN) AF: 0.378 AC: 3990 AN: 10552

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31716 AN: 67960

Other (OTH) AF: 0.441 AC: 928 AN: 2104

Alfa AF: 0.458 Hom.: 19047

Bravo AF: 0.395

Asia WGS AF: 0.256 AC: 890 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.1
DANN	Benign	0.67
PhyloP100		-0.35
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: rs1150255; hg19: chr1-207072959; COSMIC: COSV54321814; COSMIC: COSV54321814;