dbSNP rs59679449: IL11RA:c.1-212_1-201delTGTGTGTGTGTG (chr9-34654994-CGTGTGTGTGTGT-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001142784.3(IL11RA):c.1-212_1-201delTGTGTGTGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000153 in 326,526 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Exomes 𝑓: 0.000015 ( 0 hom. )

Consequence

IL11RA
NM_001142784.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.57

Publications

0 publications found

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 Gene-Disease associations (from GenCC):

craniosynostosis and dental anomalies
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet, ClinGen

IL11RA links:

ENSG00000258728 (HGNC:):

ENSG00000258728 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142784.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL11RA	NM_001142784.3	MANE Select	c.1-212_1-201delTGTGTGTGTGTG		intron	N/A	NP_001136256.1	Q14626-1
	IL11RA	NR_052010.2		n.88-212_88-201delTGTGTGTGTGTG		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IL11RA	ENST00000441545.7	TSL:5 MANE Select	c.1-212_1-201delTGTGTGTGTGTG	intron	N/A	ENSP00000394391.3	Q14626-1
IL11RA	ENST00000318041.13	TSL:1	c.1-212_1-201delTGTGTGTGTGTG	intron	N/A	ENSP00000326500.8	Q14626-1
ENSG00000258728	ENST00000556278.1	TSL:5	c.433-212_433-201delTGTGTGTGTGTG	intron	N/A	ENSP00000451792.1	G3V4G9

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.0000153

AC:

AN:

326526

Hom.:

AF XY:

0.0000172

AC XY:

AN XY:

174232

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

8820

American (AMR)

AF:

0.00

AC:

AN:

16106

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9400

East Asian (EAS)

AF:

0.0000468

AC:

AN:

21368

South Asian (SAS)

AF:

0.00

AC:

AN:

42898

European-Finnish (FIN)

AF:

0.00

AC:

AN:

20406

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1344

European-Non Finnish (NFE)

AF:

0.0000159

AC:

AN:

188150

Other (OTH)

AF:

0.0000555

AC:

AN:

18034

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

252

Bravo

AF:

0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

3.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over