rs9419541

Variant names:

• chr10-81984-A-G
• rs9419541

Your query was ambiguous. Multiple possible variants found:

• chr10-81984-A-G
• chr10-81984-A-T

Variant summary

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

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 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
IL9RP2		n.81984A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL9RP2	ENST00000423948.1	n.741+793T>C		intron_variant	Intron 6 of 6	6

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

African (AFR) AF: 0.765 AC: 31484 AN: 41178

American (AMR) AF: 0.724 AC: 11044 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2902 AN: 3470

East Asian (EAS) AF: 0.456 AC: 2347 AN: 5152

South Asian (SAS) AF: 0.666 AC: 3213 AN: 4824

European-Finnish (FIN) AF: 0.803 AC: 8501 AN: 10586

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56808 AN: 67966

Other (OTH) AF: 0.815 AC: 1721 AN: 2112

Alfa AF: 0.782 Hom.: 12531

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs9419541; hg19: chr10-127924;