9-34655737-G-T

Position:

• chr9-34655737-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001142784.3(IL11RA):​c.161+72G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 1,289,298 control chromosomes in the GnomAD database, including 113,087 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.37 (11392 hom., cov: 31)
  • Exomes 𝑓: 0.42 (101695 hom.)
• Consequence: IL11RA NM_001142784.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.290

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 9-34655737-G-T is Benign according to our data. Variant chr9-34655737-G-T is described in ClinVar as [Benign]. Clinvar id is 1231709.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL11RA	NM_001142784.3	c.161+72G>T		intron_variant		ENST00000441545.7	NP_001136256.1
IL11RA	NR_052010.2	n.248+72G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL11RA	ENST00000441545.7	c.161+72G>T		intron_variant		5	NM_001142784.3	ENSP00000394391.3
ENSG00000258728	ENST00000556278.1	c.593+72G>T		intron_variant		5		ENSP00000451792.1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56314 AN: 151696 Hom.: 11375 Cov.: 31

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.403

GnomAD4 exome AF: 0.417 AC: 473902 AN: 1137484 Hom.: 101695 Cov.: 15 AF XY: 0.416 AC XY: 241070 AN XY: 579168

Gnomad4 AFR exome AF: 0.201

Gnomad4 AMR exome AF: 0.305

Gnomad4 ASJ exome AF: 0.472

Gnomad4 EAS exome AF: 0.524

Gnomad4 SAS exome AF: 0.335

Gnomad4 FIN exome AF: 0.488

Gnomad4 NFE exome AF: 0.426

Gnomad4 OTH exome AF: 0.417

GnomAD4 genome AF: 0.371 AC: 56348 AN: 151814 Hom.: 11392 Cov.: 31 AF XY: 0.374 AC XY: 27737 AN XY: 74192

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.408

Alfa AF: 0.248 Hom.: 721

Bravo AF: 0.357

Asia WGS AF: 0.444 AC: 1544 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 16, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.40
DANN	Benign	0.51

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: rs11575576; hg19: chr9-34655734; COSMIC: COSV58841330; COSMIC: COSV58841330;