rs5916727

chrX-105162931-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_017416.2(IL1RAPL2):c.83-32544C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0106 in 111,265 control chromosomes in the GnomAD database, including 11 homozygotes. There are 296 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 0.011 (11 hom., 296 hem., cov: 22)
• Consequence: IL1RAPL2 NM_017416.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0106 (1179/111265) while in subpopulation NFE AF= 0.0169 (896/53014). AF 95% confidence interval is 0.016. There are 11 homozygotes in gnomad4. There are 296 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 11 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL1RAPL2	NM_017416.2	c.83-32544C>T		intron_variant		ENST00000372582.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL1RAPL2	ENST00000372582.6	c.83-32544C>T		intron_variant		1	NM_017416.2	P1

Frequencies

GnomAD3 genomes AF: 0.0106 AC: 1179 AN: 111209 Hom.: 11 Cov.: 22 AF XY: 0.00885 AC XY: 296 AN XY: 33431

Gnomad AFR AF: 0.00278

Gnomad AMI AF: 0.0799

Gnomad AMR AF: 0.00912

Gnomad ASJ AF: 0.00340

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00151

Gnomad FIN AF: 0.00464

Gnomad MID AF: 0.00424

Gnomad NFE AF: 0.0169

Gnomad OTH AF: 0.00474

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

GnomAD4 genome AF: 0.0106 AC: 1179 AN: 111265 Hom.: 11 Cov.: 22 AF XY: 0.00884 AC XY: 296 AN XY: 33497

Gnomad4 AFR AF: 0.00278

Gnomad4 AMR AF: 0.00911

Gnomad4 ASJ AF: 0.00340

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00152

Gnomad4 FIN AF: 0.00464

Gnomad4 NFE AF: 0.0169

Gnomad4 OTH AF: 0.00468

Alfa AF: 0.0117 Hom.: 85

Bravo AF: 0.0113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.66
Dann	Benign	0.51

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: rs5916727; hg19: chrX-104407614;