chrX-28789652-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_014271.4(IL1RAPL1):c.82+227T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 111,224 control chromosomes in the GnomAD database, including 7,837 homozygotes. There are 14,499 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.44 ( 7837 hom., 14499 hem., cov: 24)
Consequence
IL1RAPL1
NM_014271.4 intron
NM_014271.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.13
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 Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant X-28789652-T-C is Benign according to our data. Variant chrX-28789652-T-C is described in ClinVar as [Benign]. Clinvar id is 1283349.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-28789652-T-C is described in Lovd as [Likely_benign].
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL1RAPL1 | NM_014271.4 | c.82+227T>C | intron_variant | ENST00000378993.6 | |||
IL1RAPL1 | XM_017029240.2 | c.82+227T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1RAPL1 | ENST00000378993.6 | c.82+227T>C | intron_variant | 1 | NM_014271.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.440 AC: 48896AN: 111179Hom.: 7825 Cov.: 24 AF XY: 0.434 AC XY: 14483AN XY: 33383
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.440 AC: 48925AN: 111224Hom.: 7837 Cov.: 24 AF XY: 0.434 AC XY: 14499AN XY: 33438
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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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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at