9-34656482-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001142784.3(IL11RA):c.162-257G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0469 in 152,258 control chromosomes in the GnomAD database, including 257 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.047 (257 hom., cov: 32)
• Consequence: IL11RA NM_001142784.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0210

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 9-34656482-G-A is Benign according to our data. Variant chr9-34656482-G-A is described in ClinVar as [Benign]. Clinvar id is 1220727.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.063 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL11RA	NM_001142784.3	c.162-257G>A		intron_variant		ENST00000441545.7
IL11RA	NR_052010.2	n.249-257G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL11RA	ENST00000441545.7	c.162-257G>A		intron_variant		5	NM_001142784.3	P4

Frequencies

GnomAD3 genomes AF: 0.0469 AC: 7141 AN: 152140 Hom.: 256 Cov.: 32

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.0476

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.00943

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0646

Gnomad OTH AF: 0.0431

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0469 AC: 7143 AN: 152258 Hom.: 257 Cov.: 32 AF XY: 0.0467 AC XY: 3477 AN XY: 74438

Gnomad4 AFR AF: 0.0123

Gnomad4 AMR AF: 0.0476

Gnomad4 ASJ AF: 0.0473

Gnomad4 EAS AF: 0.00926

Gnomad4 SAS AF: 0.0684

Gnomad4 FIN AF: 0.0672

Gnomad4 NFE AF: 0.0646

Gnomad4 OTH AF: 0.0436

Alfa AF: 0.0567 Hom.: 45

Bravo AF: 0.0422

Asia WGS AF: 0.0350 AC: 120 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	2.4
Dann	Benign	0.80

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: rs11575578; hg19: chr9-34656479;