9-34654994-CGTGTGTGTGTGT-CGTGTGT

Variant names:

• chr9-34654994-CGTGTGT-C
• rs59679449
• NM_001142784.3:c.1-206_1-201delTGTGTG

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001142784.3(IL11RA):​c.1-206_1-201delTGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000145 in 474,986 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000020 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00020 (0 hom.)
• Consequence: IL11RA NM_001142784.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.57

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL11RA	NM_001142784.3	c.1-206_1-201delTGTGTG		intron_variant	Intron 1 of 12	ENST00000441545.7	NP_001136256.1
IL11RA	NR_052010.2	n.88-206_88-201delTGTGTG		intron_variant	Intron 1 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL11RA	ENST00000441545.7	c.1-223_1-218delGTGTGT		intron_variant	Intron 1 of 12	5	NM_001142784.3	ENSP00000394391.3
ENSG00000258728	ENST00000556278.1	c.433-223_433-218delGTGTGT		intron_variant	Intron 4 of 7	5		ENSP00000451792.1

Frequencies

GnomAD3 genomes AF: 0.0000202 AC: 3 AN: 148848 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000495

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000667

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000202 AC: 66 AN: 326138 Hom.: 0 AF XY: 0.000230 AC XY: 40 AN XY: 174038

Gnomad4 AFR exome AF: 0.000227

Gnomad4 AMR exome AF: 0.000373

Gnomad4 ASJ exome AF: 0.000213

Gnomad4 EAS exome AF: 0.000422

Gnomad4 SAS exome AF: 0.0000700

Gnomad4 FIN exome AF: 0.000147

Gnomad4 NFE exome AF: 0.000186

Gnomad4 OTH exome AF: 0.000278

GnomAD4 genome AF: 0.0000202 AC: 3 AN: 148848 Hom.: 0 Cov.: 0 AF XY: 0.0000276 AC XY: 2 AN XY: 72522

Gnomad4 AFR AF: 0.0000495

Gnomad4 AMR AF: 0.0000667

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

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;