9-34654994-CGT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001142784.3(IL11RA):c.1-202_1-201del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0826 in 440,154 control chromosomes in the GnomAD database, including 211 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.029 (118 hom., cov: 0)
  • Exomes 𝑓: 0.11 (93 hom.)
• Consequence: IL11RA NM_001142784.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0460

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 -10 ACMG points.

• BP6: Variant 9-34654994-CGT-C is Benign according to our data. Variant chr9-34654994-CGT-C is described in ClinVar as [Benign]. Clinvar id is 1251083.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL11RA	NM_001142784.3	c.1-202_1-201del		intron_variant		ENST00000441545.7
IL11RA	NR_052010.2	n.88-202_88-201del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL11RA	ENST00000441545.7	c.1-202_1-201del		intron_variant		5	NM_001142784.3	P4

Frequencies

GnomAD3 genomes AF: 0.0287 AC: 4259 AN: 148644 Hom.: 118 Cov.: 0

Gnomad AFR AF: 0.00621

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.0146

Gnomad ASJ AF: 0.0128

Gnomad EAS AF: 0.0449

Gnomad SAS AF: 0.0379

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0161

Gnomad NFE AF: 0.0307

Gnomad OTH AF: 0.0274

GnomAD4 exome AF: 0.110 AC: 32104 AN: 291428 Hom.: 93 AF XY: 0.112 AC XY: 17292 AN XY: 154970

Gnomad4 AFR exome AF: 0.0730

Gnomad4 AMR exome AF: 0.0851

Gnomad4 ASJ exome AF: 0.0665

Gnomad4 EAS exome AF: 0.187

Gnomad4 SAS exome AF: 0.126

Gnomad4 FIN exome AF: 0.163

Gnomad4 NFE exome AF: 0.0995

Gnomad4 OTH exome AF: 0.103

GnomAD4 genome AF: 0.0286 AC: 4258 AN: 148726 Hom.: 118 Cov.: 0 AF XY: 0.0322 AC XY: 2337 AN XY: 72488

Gnomad4 AFR AF: 0.00622

Gnomad4 AMR AF: 0.0146

Gnomad4 ASJ AF: 0.0128

Gnomad4 EAS AF: 0.0452

Gnomad4 SAS AF: 0.0374

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.0307

Gnomad4 OTH AF: 0.0272

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 10, 2019

- -

Computational scores

Source: dbNSFP v4.3

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: rs59679449; hg19: chr9-34654991;