9-34654994-C-CGTGT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BS1 BS2

The NM_001142784.3(IL11RA):c.1-204_1-201dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.015 (36 hom., cov: 0)
  • Exomes 𝑓: 0.0040 (1 hom.)
• Consequence: IL11RA NM_001142784.3 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.713

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-C-CGTGT is Benign according to our data. Variant chr9-34654994-C-CGTGT is described in ClinVar as [Likely_benign]. Clinvar id is 1186856.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0145 (2161/148912) while in subpopulation AFR AF= 0.046 (1865/40522). AF 95% confidence interval is 0.0443. There are 36 homozygotes in gnomad4. There are 992 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 36 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL11RA	NM_001142784.3	c.1-204_1-201dup		intron_variant		ENST00000441545.7
IL11RA	NR_052010.2	n.88-204_88-201dup		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL11RA	ENST00000441545.7	c.1-204_1-201dup		intron_variant		5	NM_001142784.3	P4

Frequencies

GnomAD3 genomes AF: 0.0145 AC: 2161 AN: 148826 Hom.: 36 Cov.: 0

Gnomad AFR AF: 0.0461

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00808

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000400

Gnomad SAS AF: 0.00553

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00645

Gnomad NFE AF: 0.00181

Gnomad OTH AF: 0.0122

GnomAD4 exome AF: 0.00400 AC: 1304 AN: 325936 Hom.: 1 Cov.: 0 AF XY: 0.00390 AC XY: 678 AN XY: 173922

Gnomad4 AFR exome AF: 0.0460

Gnomad4 AMR exome AF: 0.00535

Gnomad4 ASJ exome AF: 0.000854

Gnomad4 EAS exome AF: 0.000609

Gnomad4 SAS exome AF: 0.00523

Gnomad4 FIN exome AF: 0.000687

Gnomad4 NFE exome AF: 0.00236

Gnomad4 OTH exome AF: 0.00572

GnomAD4 genome AF: 0.0145 AC: 2161 AN: 148912 Hom.: 36 Cov.: 0 AF XY: 0.0137 AC XY: 992 AN XY: 72610

Gnomad4 AFR AF: 0.0460

Gnomad4 AMR AF: 0.00807

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000401

Gnomad4 SAS AF: 0.00554

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00181

Gnomad4 OTH AF: 0.0121

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 06, 2020

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Computational scores

Source: dbNSFP v4.3

Splicing

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;