chr9-34654994-C-CGTGTGT

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The NM_001142784.3(IL11RA):​c.1-206_1-201dupTGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0028 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0012 (0 hom.)
• Consequence: IL11RA NM_001142784.3 intron
• Clinical Significance: Not reported in ClinVar
• 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 Likely_benign. Variant got -4 ACMG points.

• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00278 (414/148934) while in subpopulation AMR AF= 0.00673 (101/15004). AF 95% confidence interval is 0.00567. There are 0 homozygotes in gnomad4. There are 224 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL11RA	NM_001142784.3	c.1-206_1-201dupTGTGTG		intron_variant	Intron 1 of 12	ENST00000441545.7	NP_001136256.1
IL11RA	NR_052010.2	n.88-206_88-201dupTGTGTG		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_1-223insGTGTGT		intron_variant	Intron 1 of 12	5	NM_001142784.3	ENSP00000394391.3
ENSG00000258728	ENST00000556278.1	c.433-224_433-223insGTGTGT		intron_variant	Intron 4 of 7	5		ENSP00000451792.1

Frequencies

GnomAD3 genomes AF: 0.00278 AC: 414 AN: 148848 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00527

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00681

Gnomad ASJ AF: 0.00437

Gnomad EAS AF: 0.00160

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00395

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000523

Gnomad OTH AF: 0.000488

GnomAD4 exome AF: 0.00121 AC: 394 AN: 326482 Hom.: 0 Cov.: 0 AF XY: 0.00110 AC XY: 192 AN XY: 174212

Gnomad4 AFR exome AF: 0.00397

Gnomad4 AMR exome AF: 0.00882

Gnomad4 ASJ exome AF: 0.00223

Gnomad4 EAS exome AF: 0.00351

Gnomad4 SAS exome AF: 0.000210

Gnomad4 FIN exome AF: 0.00132

Gnomad4 NFE exome AF: 0.000303

Gnomad4 OTH exome AF: 0.00155

GnomAD4 genome AF: 0.00278 AC: 414 AN: 148934 Hom.: 0 Cov.: 0 AF XY: 0.00308 AC XY: 224 AN XY: 72620

Gnomad4 AFR AF: 0.00528

Gnomad4 AMR AF: 0.00673

Gnomad4 ASJ AF: 0.00437

Gnomad4 EAS AF: 0.00160

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00395

Gnomad4 NFE AF: 0.000523

Gnomad4 OTH AF: 0.000484

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;