X-105023319-C-T

Variant names:

• chrX-105023319-C-T
• rs985425
• NM_017416.2:c.83-172156C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_017416.2(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 NM_017416.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734
• Publications: 1 publications found

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

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1RAPL2	NM_017416.2	c.83-172156C>T		intron_variant	Intron 2 of 10	ENST00000372582.6	NP_059112.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1RAPL2	ENST00000372582.6	c.83-172156C>T		intron_variant	Intron 2 of 10	1	NM_017416.2	ENSP00000361663.1

Frequencies

GnomAD3 genomes AF: 0.550 AC: 60320 AN: 109602 Hom.: 12088 Cov.: 22

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

African (AFR) AF: 0.548 AC: 16585 AN: 30251

American (AMR) AF: 0.490 AC: 5048 AN: 10300

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 1549 AN: 2616

East Asian (EAS) AF: 0.746 AC: 2554 AN: 3424

South Asian (SAS) AF: 0.383 AC: 1005 AN: 2621

European-Finnish (FIN) AF: 0.502 AC: 2878 AN: 5730

Middle Eastern (MID) AF: 0.443 AC: 93 AN: 210

European-Non Finnish (NFE) AF: 0.561 AC: 29372 AN: 52345

Other (OTH) AF: 0.540 AC: 803 AN: 1486

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
PhyloP100		0.73
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs985425; hg19: chrX-104268001;