X-28855378-C-T

Variant names:

• chrX-28855378-C-T
• rs1318832
• NM_014271.4:c.82+65953C>T

Variant summary

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

The NM_014271.4(IL1RAPL1):​c.82+65953C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 108,574 control chromosomes in the GnomAD database, including 12,379 homozygotes. There are 15,821 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 0.52 (12379 hom., 15821 hem., cov: 21)
• Consequence: IL1RAPL1 NM_014271.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1RAPL1	NM_014271.4	c.82+65953C>T		intron_variant	Intron 2 of 10	ENST00000378993.6	NP_055086.1
IL1RAPL1	XM_017029240.2	c.82+65953C>T		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+65953C>T		intron_variant	Intron 2 of 10	1	NM_014271.4	ENSP00000368278.1

Frequencies

GnomAD3 genomes AF: 0.519 AC: 56330 AN: 108528 Hom.: 12370 Cov.: 21 AF XY: 0.511 AC XY: 15791 AN XY: 30900

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.519 AC: 56375 AN: 108574 Hom.: 12379 Cov.: 21 AF XY: 0.511 AC XY: 15821 AN XY: 30956

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.806

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.508

Alfa AF: 0.439 Hom.: 4049

Bravo AF: 0.556

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.83
DANN	Benign	0.57

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: rs1318832; hg19: chrX-28873495;