Variant chr9-34655439-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001142784.3(IL11RA):c.100+122T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 861,380 control chromosomes in the GnomAD database, including 147,377 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.59 ( 26199 hom., cov: 30)

Exomes 𝑓: 0.58 ( 121178 hom. )

Consequence

IL11RA
NM_001142784.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0440

Variant links:

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]

IL11RA links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 9-34655439-T-C is Benign according to our data. Variant chr9-34655439-T-C is described in ClinVar as [Benign]. Clinvar id is 1179216.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL11RA	NM_001142784.3 linkuse as main transcript	c.100+122T>C		intron_variant		ENST00000441545.7
IL11RA	NR_052010.2 linkuse as main transcript	n.187+122T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL11RA	ENST00000441545.7 linkuse as main transcript	c.100+122T>C		intron_variant		5	NM_001142784.3	P4	Q14626-1

Frequencies

GnomAD3 genomes

AF:

0.586

AC:

89008

AN:

151864

Hom.:

26164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.595

Gnomad AMI

AF:

0.518

Gnomad AMR

AF:

0.516

Gnomad ASJ

AF:

0.628

Gnomad EAS

AF:

0.533

Gnomad SAS

AF:

0.559

Gnomad FIN

AF:

0.653

Gnomad MID

AF:

0.592

Gnomad NFE

AF:

0.591

Gnomad OTH

AF:

0.589

GnomAD4 exome

AF:

0.582

AC:

412662

AN:

709398

Hom.:

121178

Cov.:

AF XY:

0.581

AC XY:

217528

AN XY:

374450

show subpopulations

Gnomad4 AFR exome

AF:

0.591

Gnomad4 AMR exome

AF:

0.430

Gnomad4 ASJ exome

AF:

0.629

Gnomad4 EAS exome

AF:

0.535

Gnomad4 SAS exome

AF:

0.557

Gnomad4 FIN exome

AF:

0.648

Gnomad4 NFE exome

AF:

0.590

Gnomad4 OTH exome

AF:

0.593

GnomAD4 genome

AF:

0.586

AC:

89100

AN:

151982

Hom.:

26199

Cov.:

AF XY:

0.586

AC XY:

43536

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.595

Gnomad4 AMR

AF:

0.516

Gnomad4 ASJ

AF:

0.628

Gnomad4 EAS

AF:

0.533

Gnomad4 SAS

AF:

0.559

Gnomad4 FIN

AF:

0.653

Gnomad4 NFE

AF:

0.591

Gnomad4 OTH

AF:

0.592

Alfa

AF:

0.583

Hom.:

32864

Bravo

AF:

0.575

Asia WGS

AF:

0.565

AC:

1962

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

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

-0.85

CADD

Benign

2.3

DANN

Benign

0.86

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over