5-135894564-G-T

Variant names:

• chr5-135894564-G-T
• rs31564
• NM_000590.2:c.184-413C>A

Variant summary

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

The NM_000590.2(IL9):​c.184-413C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 152,100 control chromosomes in the GnomAD database, including 33,324 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 0.66 (33324 hom., cov: 32)
• Consequence: IL9 NM_000590.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 29 publications found

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

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 = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL9	NM_000590.2	c.184-413C>A		intron_variant	Intron 3 of 4	ENST00000274520.2	NP_000581.1
LOC124901074	XR_007058947.1	n.509-1134G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL9	ENST00000274520.2	c.184-413C>A		intron_variant	Intron 3 of 4	1	NM_000590.2	ENSP00000274520.1

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99876 AN: 151980 Hom.: 33298 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.657 AC: 99952 AN: 152100 Hom.: 33324 Cov.: 32 AF XY: 0.653 AC XY: 48570 AN XY: 74352

African (AFR) AF: 0.763 AC: 31683 AN: 41510

American (AMR) AF: 0.650 AC: 9936 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2198 AN: 3468

East Asian (EAS) AF: 0.455 AC: 2354 AN: 5172

South Asian (SAS) AF: 0.554 AC: 2672 AN: 4820

European-Finnish (FIN) AF: 0.615 AC: 6502 AN: 10566

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42495 AN: 67966

Other (OTH) AF: 0.645 AC: 1360 AN: 2108

Alfa AF: 0.630 Hom.: 59254

Bravo AF: 0.666

Asia WGS AF: 0.507 AC: 1761 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	0.17
DANN	Benign	0.30
PhyloP100		-1.5
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: rs31564; hg19: chr5-135230253;