X-29134105-A-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_014271.4(IL1RAPL1):c.83-148833A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., 0 hem., cov: 23)
Failed GnomAD Quality Control
Consequence
IL1RAPL1
NM_014271.4 intron
NM_014271.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0550
Publications
0 publications found
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]
IL1RAPL1 Gene-Disease associations (from GenCC):
- intellectual disability, X-linked 21Inheritance: XL Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
- non-syndromic X-linked intellectual disabilityInheritance: XL Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_014271.4. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 110671Hom.: 0 Cov.: 23
GnomAD3 genomes
AF:
AC:
0
AN:
110671
Hom.:
Cov.:
23
Gnomad AFR
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Gnomad AMI
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Gnomad AMR
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Gnomad ASJ
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Gnomad EAS
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Gnomad FIN
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Gnomad NFE
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Gnomad OTH
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.00 AC: 0AN: 110671Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 32883
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
110671
Hom.:
Cov.:
23
AF XY:
AC XY:
0
AN XY:
32883
African (AFR)
AF:
AC:
0
AN:
30471
American (AMR)
AF:
AC:
0
AN:
10304
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2633
East Asian (EAS)
AF:
AC:
0
AN:
3539
South Asian (SAS)
AF:
AC:
0
AN:
2613
European-Finnish (FIN)
AF:
AC:
0
AN:
5870
Middle Eastern (MID)
AF:
AC:
0
AN:
237
European-Non Finnish (NFE)
AF:
AC:
0
AN:
52849
Other (OTH)
AF:
AC:
0
AN:
1476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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