chrX-105023319-C-T

Position:

• chrX-105023319-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000372582.6(IL1RAPL2):​c.83-172156C>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 0.55 (12084 hom., 17303 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: IL1RAPL2 ENST00000372582.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734

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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL1RAPL2	NM_017416.2	c.83-172156C>T		intron_variant		ENST00000372582.6	NP_059112.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1RAPL2	ENST00000372582.6	c.83-172156C>T		intron_variant		1	NM_017416.2	ENSP00000361663	P1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 60320 AN: 109602 Hom.: 12088 Cov.: 22 AF XY: 0.538 AC XY: 17267 AN XY: 32092

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.536

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: 0.550 AC: 60339 AN: 109652 Hom.: 12084 Cov.: 22 AF XY: 0.538 AC XY: 17303 AN XY: 32152

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.540

Alfa AF: 0.554 Hom.: 6916

Bravo AF: 0.552

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
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: rs985425; hg19: chrX-104268001;