rs2399153

Variant names:

• chr22-17012403-A-G
• rs2399153
• ENST00000605217.1:n.-1A>G

Your query was ambiguous. Multiple possible variants found:

• chr22-17012403-A-G
• chr22-17012403-A-T

Variant summary

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

The ENST00000605217.1(IL9RP6):​n.-1A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 153,664 control chromosomes in the GnomAD database, including 59,617 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 0.88 (59084 hom., cov: 31)
  • Exomes 𝑓: 0.83 (533 hom.)
• Consequence: IL9RP6 ENST00000605217.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 4 publications found

Genes affected

IL9RP6 (HGNC:56970):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL9RP6	ENST00000605217.1	n.-1A>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133659 AN: 152032 Hom.: 59030 Cov.: 31

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.872

GnomAD4 exome AF: 0.830 AC: 1256 AN: 1514 Hom.: 533 Cov.: 0 AF XY: 0.840 AC XY: 746 AN XY: 888

African (AFR) AF: 1.00 AC: 18 AN: 18

American (AMR) AF: 1.00 AC: 6 AN: 6

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 9 AN: 10

East Asian (EAS) AF: 0.750 AC: 9 AN: 12

South Asian (SAS) AF: 0.799 AC: 615 AN: 770

European-Finnish (FIN) AF: 0.869 AC: 113 AN: 130

Middle Eastern (MID) AF: 0.875 AC: 7 AN: 8

European-Non Finnish (NFE) AF: 0.867 AC: 430 AN: 496

Other (OTH) AF: 0.766 AC: 49 AN: 64

GnomAD4 genome AF: 0.879 AC: 133776 AN: 152150 Hom.: 59084 Cov.: 31 AF XY: 0.883 AC XY: 65631 AN XY: 74362

African (AFR) AF: 0.969 AC: 40279 AN: 41552

American (AMR) AF: 0.867 AC: 13262 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2908 AN: 3470

East Asian (EAS) AF: 0.840 AC: 4299 AN: 5120

South Asian (SAS) AF: 0.815 AC: 3925 AN: 4818

European-Finnish (FIN) AF: 0.903 AC: 9578 AN: 10608

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56691 AN: 67972

Other (OTH) AF: 0.870 AC: 1832 AN: 2106

Alfa AF: 0.845 Hom.: 92950

Bravo AF: 0.882

Asia WGS AF: 0.801 AC: 2785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	15
DANN	Benign	0.25
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2399153; hg19: chr22-17493293;