chrX-28789631-A-G
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_014271.4(IL1RAPL1):c.82+206A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.63 ( 17139 hom., 20792 hem., cov: 23)
Failed GnomAD Quality Control
Consequence
IL1RAPL1
NM_014271.4 intron
NM_014271.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.259
Genes affected
IL1RAPL1 (HGNC:5996): (interleukin 1 receptor accessory protein like 1) The protein encoded by this gene is a member of the interleukin 1 receptor family and is similar to the interleukin 1 accessory proteins. This protein has an N-terminal signal peptide, three extracellular immunoglobulin Ig-like domains, a transmembrane domain, an intracellular Toll/IL-1R domain, and a long C-terminal tail which interacts with multiple signalling molecules. This gene is located at a region on chromosome X that is associated with a non-syndromic form of X-linked intellectual disability. Deletions and mutations in this gene were found in patients with intellectual disability. This gene is expressed at a high level in post-natal brain structures involved in the hippocampal memory system, which suggests a specialized role in the physiological processes underlying memory and learning abilities, and plays a role in synapse formation and stabilization. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant X-28789631-A-G is Benign according to our data. Variant chrX-28789631-A-G is described in ClinVar as [Benign]. Clinvar id is 1237882.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-28789631-A-G is described in Lovd as [Likely_benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL1RAPL1 | NM_014271.4 | c.82+206A>G | intron_variant | ENST00000378993.6 | |||
IL1RAPL1 | XM_017029240.2 | c.82+206A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1RAPL1 | ENST00000378993.6 | c.82+206A>G | intron_variant | 1 | NM_014271.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.631 AC: 70097AN: 111003Hom.: 17126 Cov.: 23 AF XY: 0.625 AC XY: 20752AN XY: 33215
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.632 AC: 70152AN: 111048Hom.: 17139 Cov.: 23 AF XY: 0.625 AC XY: 20792AN XY: 33270
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 03, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at