rs9419541

chr10-81984-A-Gchr10-81984-A-T

Variant summary

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

The ENST00000423948.1(IL9RP2):n.741+793T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.785 in 151,752 control chromosomes in the GnomAD database, including 47,246 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 0.79 (47246 hom., cov: 34)
• Consequence: IL9RP2 ENST00000423948.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

Genes affected

IL9RP2 (HGNC:6032): (IL9R pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL9RP2	ENST00000423948.1	n.741+793T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119075 AN: 151640 Hom.: 47212 Cov.: 34

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.955

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.785 AC: 119150 AN: 151752 Hom.: 47246 Cov.: 34 AF XY: 0.780 AC XY: 57878 AN XY: 74184

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.666

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.815

Alfa AF: 0.793 Hom.: 4610

Bravo AF: 0.772

Asia WGS AF: 0.609 AC: 2121 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.79
Dann	Benign	0.11

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9419541; hg19: chr10-127924;