9-34655299-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5
The NM_001142784.3(IL11RA):c.82C>T(p.Gln28*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000481 in 1,453,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001142784.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.0000166 AC: 4AN: 240388Hom.: 0 AF XY: 0.0000230 AC XY: 3AN XY: 130348
GnomAD4 exome AF: 0.00000481 AC: 7AN: 1453852Hom.: 0 Cov.: 30 AF XY: 0.00000830 AC XY: 6AN XY: 723176
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not provided Pathogenic:1Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Mar 05, 2024 | Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Has not been previously published as pathogenic or benign to our knowledge - |
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 08, 2024 | This sequence change creates a premature translational stop signal (p.Gln28*) in the IL11RA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in IL11RA are known to be pathogenic (PMID: 21741611, 24498618). This variant is present in population databases (rs774749917, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with IL11RA-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at