9-34654994-CGTGTGTGTGTGT-CGTGTGTGTGTGTGT

Variant names:

• chr9-34654994-C-CGT
• rs59679449
• NM_001142784.3:c.1-202_1-201dupTG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001142784.3(IL11RA):​c.1-202_1-201dupTG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.35 (9343 hom., cov: 0)
  • Exomes 𝑓: 0.28 (1103 hom.)
• Consequence: IL11RA NM_001142784.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.713
• Publications: 0 publications found

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

ENSG00000258728 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 9-34654994-C-CGT is Benign according to our data. Variant chr9-34654994-C-CGT is described in ClinVar as Benign. ClinVar VariationId is 1279224.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

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.1-202_1-201dupTG		intron	N/A	NP_001136256.1	Q14626-1
	IL11RA	NR_052010.2		n.88-202_88-201dupTG		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL11RA	ENST00000441545.7	TSL:5 MANE Select	c.1-202_1-201dupTG		intron	N/A	ENSP00000394391.3	Q14626-1
	IL11RA	ENST00000318041.13	TSL:1	c.1-202_1-201dupTG		intron	N/A	ENSP00000326500.8	Q14626-1
	ENSG00000258728	ENST00000556278.1	TSL:5	c.433-202_433-201dupTG		intron	N/A	ENSP00000451792.1	G3V4G9

Frequencies

GnomAD3 genomes AF: 0.351 AC: 52219 AN: 148686 Hom.: 9338 Cov.: 0

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.379

GnomAD4 exome AF: 0.280 AC: 90326 AN: 322530 Hom.: 1103 Cov.: 0 AF XY: 0.279 AC XY: 48005 AN XY: 172006

African (AFR) AF: 0.253 AC: 2207 AN: 8734

American (AMR) AF: 0.280 AC: 4449 AN: 15882

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 3243 AN: 9304

East Asian (EAS) AF: 0.123 AC: 2594 AN: 21130

South Asian (SAS) AF: 0.256 AC: 10853 AN: 42324

European-Finnish (FIN) AF: 0.267 AC: 5376 AN: 20162

Middle Eastern (MID) AF: 0.341 AC: 452 AN: 1326

European-Non Finnish (NFE) AF: 0.301 AC: 55997 AN: 185882

Other (OTH) AF: 0.290 AC: 5155 AN: 17786

GnomAD4 genome AF: 0.351 AC: 52251 AN: 148772 Hom.: 9343 Cov.: 0 AF XY: 0.345 AC XY: 25039 AN XY: 72534

African (AFR) AF: 0.307 AC: 12411 AN: 40482

American (AMR) AF: 0.355 AC: 5324 AN: 14996

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1659 AN: 3428

East Asian (EAS) AF: 0.146 AC: 729 AN: 4988

South Asian (SAS) AF: 0.289 AC: 1351 AN: 4678

European-Finnish (FIN) AF: 0.331 AC: 3345 AN: 10102

Middle Eastern (MID) AF: 0.465 AC: 134 AN: 288

European-Non Finnish (NFE) AF: 0.393 AC: 26268 AN: 66852

Other (OTH) AF: 0.375 AC: 774 AN: 2062

Alfa AF: 0.140 Hom.: 252

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.71
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs59679449; hg19: chr9-34654991;