5-135893944-T-C

Position:

• chr5-135893944-T-C

Variant summary

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

The NM_000590.2(IL9):​c.315+76A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 1,245,016 control chromosomes in the GnomAD database, including 27,734 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 0.24 (4698 hom., cov: 32)
  • Exomes 𝑓: 0.20 (23036 hom.)
• Consequence: IL9 NM_000590.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

Genes affected

IL9 (HGNC:6029): (interleukin 9) The protein encoded by this gene is a cytokine that acts as a regulator of a variety of hematopoietic cells. This cytokine stimulates cell proliferation and prevents apoptosis. It functions through the interleukin 9 receptor (IL9R), which activates different signal transducer and activator (STAT) proteins and thus connects this cytokine to various biological processes. The gene encoding this cytokine has been identified as a candidate gene for asthma. Genetic studies on a mouse model of asthma demonstrated that this cytokine is a determining factor in the pathogenesis of bronchial hyperresponsiveness. [provided by RefSeq, Jul 2008]

LOC124901074 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL9	NM_000590.2	c.315+76A>G		intron_variant		ENST00000274520.2	NP_000581.1
LOC124901074	XR_007058947.1	n.508+1341T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL9	ENST00000274520.2	c.315+76A>G		intron_variant		1	NM_000590.2	ENSP00000274520.1

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35752 AN: 152044 Hom.: 4683 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0386

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.235

GnomAD4 exome AF: 0.198 AC: 215864 AN: 1092854 Hom.: 23036 AF XY: 0.197 AC XY: 107984 AN XY: 548140

Gnomad4 AFR exome AF: 0.358

Gnomad4 AMR exome AF: 0.118

Gnomad4 ASJ exome AF: 0.345

Gnomad4 EAS exome AF: 0.0618

Gnomad4 SAS exome AF: 0.158

Gnomad4 FIN exome AF: 0.194

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.209

GnomAD4 genome AF: 0.235 AC: 35802 AN: 152162 Hom.: 4698 Cov.: 32 AF XY: 0.232 AC XY: 17238 AN XY: 74384

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.0387

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.233

Alfa AF: 0.210 Hom.: 1801

Bravo AF: 0.238

Asia WGS AF: 0.126 AC: 442 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	2.8
DANN	Benign	0.25

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: rs2069882; hg19: chr5-135229633;