chrX-28789631-A-G

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

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.259
Variant links:
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
IL1RAPL1NM_014271.4 linkuse as main transcriptc.82+206A>G intron_variant ENST00000378993.6
IL1RAPL1XM_017029240.2 linkuse as main transcriptc.82+206A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL1RAPL1ENST00000378993.6 linkuse as main transcriptc.82+206A>G intron_variant 1 NM_014271.4 P1Q9NZN1-1

Frequencies

GnomAD3 genomes
AF:
0.631
AC:
70097
AN:
111003
Hom.:
17126
Cov.:
23
AF XY:
0.625
AC XY:
20752
AN XY:
33215
show subpopulations
Gnomad AFR
AF:
0.908
Gnomad AMI
AF:
0.340
Gnomad AMR
AF:
0.599
Gnomad ASJ
AF:
0.654
Gnomad EAS
AF:
0.847
Gnomad SAS
AF:
0.629
Gnomad FIN
AF:
0.456
Gnomad MID
AF:
0.678
Gnomad NFE
AF:
0.486
Gnomad OTH
AF:
0.630
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:
70152
AN:
111048
Hom.:
17139
Cov.:
23
AF XY:
0.625
AC XY:
20792
AN XY:
33270
show subpopulations
Gnomad4 AFR
AF:
0.908
Gnomad4 AMR
AF:
0.599
Gnomad4 ASJ
AF:
0.654
Gnomad4 EAS
AF:
0.846
Gnomad4 SAS
AF:
0.630
Gnomad4 FIN
AF:
0.456
Gnomad4 NFE
AF:
0.486
Gnomad4 OTH
AF:
0.634
Alfa
AF:
0.571
Hom.:
6287
Bravo
AF:
0.660

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 submitterclinical testingGeneDxJul 03, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.57
DANN
Benign
0.35

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6526807; hg19: chrX-28807748; API