chr9-34655316-A-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP3BP6_Moderate
The NM_001142784.3(IL11RA):c.99A>C(p.Pro33=) variant causes a splice region, synonymous change. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000033 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
IL11RA
NM_001142784.3 splice_region, synonymous
NM_001142784.3 splice_region, synonymous
Scores
2
Splicing: ADA: 0.9715
2
Clinical Significance
Conservation
PhyloP100: 3.59
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PP3
?
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. Scorers claiming Uncertain: max_spliceai. No scorers claiming Benign.
BP6
?
Variant 9-34655316-A-C is Benign according to our data. Variant chr9-34655316-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 3039737.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL11RA | NM_001142784.3 | c.99A>C | p.Pro33= | splice_region_variant, synonymous_variant | 2/13 | ENST00000441545.7 | |
IL11RA | NR_052010.2 | n.186A>C | splice_region_variant, non_coding_transcript_exon_variant | 2/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL11RA | ENST00000441545.7 | c.99A>C | p.Pro33= | splice_region_variant, synonymous_variant | 2/13 | 5 | NM_001142784.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 149344Hom.: 0 Cov.: 30 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000333 AC: 45AN: 1352024Hom.: 0 Cov.: 25 AF XY: 0.0000207 AC XY: 14AN XY: 676138
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GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 149472Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 73008
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
IL11RA-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 16, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DL_spliceai
Position offset: 1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at