rs10521948

Variant names:

• chrX-28821786-G-A
• rs10521948
• NM_014271.4:c.82+32361G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014271.4(IL1RAPL1):​c.82+32361G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 110,744 control chromosomes in the GnomAD database, including 567 homozygotes. There are 3,560 hemizygotes in GnomAD. 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 0.11 (567 hom., 3560 hem., cov: 22)
• Consequence: IL1RAPL1 NM_014271.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1RAPL1	NM_014271.4	c.82+32361G>A		intron_variant	Intron 2 of 10	ENST00000378993.6	NP_055086.1
IL1RAPL1	XM_017029240.2	c.82+32361G>A		intron_variant	Intron 2 of 10		XP_016884729.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1RAPL1	ENST00000378993.6	c.82+32361G>A		intron_variant	Intron 2 of 10	1	NM_014271.4	ENSP00000368278.1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 12616 AN: 110690 Hom.: 568 Cov.: 22 AF XY: 0.108 AC XY: 3550 AN XY: 33016

Gnomad AFR AF: 0.0923

Gnomad AMI AF: 0.0591

Gnomad AMR AF: 0.0796

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0623

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.0930

Gnomad MID AF: 0.267

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.130

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.114 AC: 12625 AN: 110744 Hom.: 567 Cov.: 22 AF XY: 0.108 AC XY: 3560 AN XY: 33080

Gnomad4 AFR AF: 0.0925

Gnomad4 AMR AF: 0.0795

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.0622

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.0930

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.134

Alfa AF: 0.136 Hom.: 2460

Bravo AF: 0.108

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.64

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

Other links and lift over

dbSNP: rs10521948; hg19: chrX-28839903;