rs1859430

Variant names:

• chr5-135894824-G-A
• rs1859430
• NM_000590.2:c.183+616C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-135894824-G-A
• chr5-135894824-G-C
• chr5-135894824-G-T

Variant summary

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

The NM_000590.2(IL9):​c.183+616C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,118 control chromosomes in the GnomAD database, including 3,162 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 0.20 (3162 hom., cov: 32)
• Consequence: IL9 NM_000590.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 22 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL9	NM_000590.2	c.183+616C>T		intron_variant	Intron 3 of 4	ENST00000274520.2	NP_000581.1
LOC124901074	XR_007058947.1	n.509-874G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL9	ENST00000274520.2	c.183+616C>T		intron_variant	Intron 3 of 4	1	NM_000590.2	ENSP00000274520.1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30058 AN: 152000 Hom.: 3154 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0386

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.198 AC: 30097 AN: 152118 Hom.: 3162 Cov.: 32 AF XY: 0.195 AC XY: 14504 AN XY: 74364

African (AFR) AF: 0.259 AC: 10757 AN: 41488

American (AMR) AF: 0.142 AC: 2167 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3470

East Asian (EAS) AF: 0.0387 AC: 200 AN: 5170

South Asian (SAS) AF: 0.133 AC: 641 AN: 4818

European-Finnish (FIN) AF: 0.183 AC: 1942 AN: 10588

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12950 AN: 67978

Other (OTH) AF: 0.190 AC: 400 AN: 2110

Alfa AF: 0.192 Hom.: 12390

Bravo AF: 0.196

Asia WGS AF: 0.115 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.48
PhyloP100		-0.13
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: rs1859430; hg19: chr5-135230513;