chrX-105752161-C-T

Position:

• chrX-105752161-C-T

Variant summary

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

The NM_017416.2(IL1RAPL2):​c.1193-3016C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 110,936 control chromosomes in the GnomAD database, including 747 homozygotes. There are 4,015 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 0.13 (747 hom., 4015 hem., cov: 23)
• Consequence: IL1RAPL2 NM_017416.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464

Genes affected

IL1RAPL2 (HGNC:5997): (interleukin 1 receptor accessory protein like 2) The protein encoded by this gene is a member of the interleukin 1 receptor family. This protein is similar to the interleukin 1 accessory proteins, and is most closely related to interleukin 1 receptor accessory protein-like 1 (IL1RAPL1). This gene and IL1RAPL1 are located at a region on chromosome X that is associated with X-linked non-syndromic cognitive disability. [provided by RefSeq, Jul 2008]

LOC105373303 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1RAPL2	NM_017416.2	c.1193-3016C>T		intron_variant		ENST00000372582.6	NP_059112.1
LOC105373303	XR_938493.3	n.356+21127G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1RAPL2	ENST00000372582.6	c.1193-3016C>T		intron_variant		1	NM_017416.2	ENSP00000361663	P1
IL1RAPL2	ENST00000485671.1	n.188-3016C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.125 AC: 13876 AN: 110882 Hom.: 747 Cov.: 23 AF XY: 0.121 AC XY: 4009 AN XY: 33152

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.0802

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.0657

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.125 AC: 13885 AN: 110936 Hom.: 747 Cov.: 23 AF XY: 0.121 AC XY: 4015 AN XY: 33216

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.0802

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.0657

Gnomad4 NFE AF: 0.0849

Gnomad4 OTH AF: 0.116

Alfa AF: 0.112 Hom.: 2067

Bravo AF: 0.130

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.2
DANN	Benign	0.73

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: rs9887672; hg19: chrX-104996155;