9-34654994-CGTGTGTGTGTGT-CGTGTGTGTGTGTGT

Variant names:

• chr9-34654994-C-CGT
• rs59679449
• NM_001142784.3:c.1-202_1-201dupTG

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_1-201dupTG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.35 (9343 hom., cov: 0)
  • Exomes 𝑓: 0.28 (1103 hom.)
• Consequence: IL11RA NM_001142784.3 intron
• Clinical Significance: 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]

ENSG00000258728 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 9-34654994-C-CGT is Benign according to our data. Variant chr9-34654994-C-CGT is described in ClinVar as [Benign]. Clinvar id is 1279224.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL11RA	NM_001142784.3	c.1-202_1-201dupTG		intron_variant	Intron 1 of 12	ENST00000441545.7	NP_001136256.1
IL11RA	NR_052010.2	n.88-202_88-201dupTG		intron_variant	Intron 1 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL11RA	ENST00000441545.7	c.1-224_1-223insGT		intron_variant	Intron 1 of 12	5	NM_001142784.3	ENSP00000394391.3
ENSG00000258728	ENST00000556278.1	c.433-224_433-223insGT		intron_variant	Intron 4 of 7	5		ENSP00000451792.1

Frequencies

GnomAD3 genomes AF: 0.351 AC: 52219 AN: 148686 Hom.: 9338 Cov.: 0

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.379

GnomAD4 exome AF: 0.280 AC: 90326 AN: 322530 Hom.: 1103 Cov.: 0 AF XY: 0.279 AC XY: 48005 AN XY: 172006

Gnomad4 AFR exome AF: 0.253

Gnomad4 AMR exome AF: 0.280

Gnomad4 ASJ exome AF: 0.349

Gnomad4 EAS exome AF: 0.123

Gnomad4 SAS exome AF: 0.256

Gnomad4 FIN exome AF: 0.267

Gnomad4 NFE exome AF: 0.301

Gnomad4 OTH exome AF: 0.290

GnomAD4 genome AF: 0.351 AC: 52251 AN: 148772 Hom.: 9343 Cov.: 0 AF XY: 0.345 AC XY: 25039 AN XY: 72534

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.375

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Aug 26, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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;