rs1061758

Positions:

• chr9-34652333-A-G

Variant summary

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

The NM_001142784.3(IL11RA):​c.-1+100A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 153,394 control chromosomes in the GnomAD database, including 45,398 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 0.76 (44883 hom., cov: 31)
  • Exomes 𝑓: 0.87 (515 hom.)
• Consequence: IL11RA NM_001142784.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.895

Genes affected

IL11RA (HGNC:5967): (interleukin 11 receptor subunit alpha) Interleukin 11 is a stromal cell-derived cytokine that belongs to a family of pleiotropic and redundant cytokines that use the gp130 transducing subunit in their high affinity receptors. This gene encodes the IL-11 receptor, which is a member of the hematopoietic cytokine receptor family. This particular receptor is very similar to ciliary neurotrophic factor, since both contain an extracellular region with a 2-domain structure composed of an immunoglobulin-like domain and a cytokine receptor-like domain. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL11RA	NM_001142784.3	c.-1+100A>G		intron_variant		ENST00000441545.7	NP_001136256.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL11RA	ENST00000441545.7	c.-1+100A>G		intron_variant		5	NM_001142784.3	ENSP00000394391	P4

Frequencies

GnomAD3 genomes AF: 0.763 AC: 115895 AN: 151910 Hom.: 44844 Cov.: 31

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.765

GnomAD4 exome AF: 0.867 AC: 1184 AN: 1366 Hom.: 515 AF XY: 0.862 AC XY: 674 AN XY: 782

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.750

Gnomad4 EAS exome AF: 0.375

Gnomad4 SAS exome AF: 0.944

Gnomad4 FIN exome AF: 0.875

Gnomad4 NFE exome AF: 0.851

Gnomad4 OTH exome AF: 0.794

GnomAD4 genome AF: 0.763 AC: 115990 AN: 152028 Hom.: 44883 Cov.: 31 AF XY: 0.764 AC XY: 56771 AN XY: 74316

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.860

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.872

Gnomad4 NFE AF: 0.834

Gnomad4 OTH AF: 0.768

Alfa AF: 0.816 Hom.: 85089

Bravo AF: 0.741

Asia WGS AF: 0.701 AC: 2437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	9.0
DANN	Benign	0.80
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.1

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

Publications

LitVar

Other links and lift over

dbSNP: rs1061758; hg19: chr9-34652330; COSMIC: COSV58841653; COSMIC: COSV58841653;