chr9-34654994-C-CGTGT
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001142784.3(IL11RA):c.1-204_1-201dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.015 ( 36 hom., cov: 0)
Exomes 𝑓: 0.0040 ( 1 hom. )
Consequence
IL11RA
NM_001142784.3 intron
NM_001142784.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.713
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 9-34654994-C-CGTGT is Benign according to our data. Variant chr9-34654994-C-CGTGT is described in ClinVar as [Likely_benign]. Clinvar id is 1186856.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0145 (2161/148912) while in subpopulation AFR AF= 0.046 (1865/40522). AF 95% confidence interval is 0.0443. There are 36 homozygotes in gnomad4. There are 992 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 36 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL11RA | NM_001142784.3 | c.1-204_1-201dup | intron_variant | ENST00000441545.7 | |||
IL11RA | NR_052010.2 | n.88-204_88-201dup | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL11RA | ENST00000441545.7 | c.1-204_1-201dup | intron_variant | 5 | NM_001142784.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0145 AC: 2161AN: 148826Hom.: 36 Cov.: 0
GnomAD3 genomes
?
AF:
AC:
2161
AN:
148826
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00400 AC: 1304AN: 325936Hom.: 1 Cov.: 0 AF XY: 0.00390 AC XY: 678AN XY: 173922
GnomAD4 exome
AF:
AC:
1304
AN:
325936
Hom.:
Cov.:
0
AF XY:
AC XY:
678
AN XY:
173922
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0145 AC: 2161AN: 148912Hom.: 36 Cov.: 0 AF XY: 0.0137 AC XY: 992AN XY: 72610
GnomAD4 genome
?
AF:
AC:
2161
AN:
148912
Hom.:
Cov.:
0
AF XY:
AC XY:
992
AN XY:
72610
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 06, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at