rs210426

chrX-105690173-G-AchrX-105690173-G-C

Variant summary

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

The NM_017416.2(IL1RAPL2):c.773-27194G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00816 in 110,247 control chromosomes in the GnomAD database, including 10 homozygotes. There are 301 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 0.0082 (10 hom., 301 hem., cov: 22)
• Consequence: IL1RAPL2 NM_017416.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924

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=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL1RAPL2	NM_017416.2	c.773-27194G>A		intron_variant		ENST00000372582.6
LOC105373303	XR_938493.3	n.663-26981C>T		intron_variant, non_coding_transcript_variant
IL1RAPL2	XM_011530905.3	c.401-27194G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL1RAPL2	ENST00000372582.6	c.773-27194G>A		intron_variant		1	NM_017416.2	P1

Frequencies

GnomAD3 genomes AF: 0.00817 AC: 900 AN: 110199 Hom.: 10 Cov.: 22 AF XY: 0.00923 AC XY: 300 AN XY: 32497

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.0119

Gnomad AMR AF: 0.00301

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0492

Gnomad SAS AF: 0.0679

Gnomad FIN AF: 0.00171

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00222

Gnomad OTH AF: 0.00541

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

GnomAD4 genome AF: 0.00816 AC: 900 AN: 110247 Hom.: 10 Cov.: 22 AF XY: 0.00925 AC XY: 301 AN XY: 32555

Gnomad4 AFR AF: 0.0126

Gnomad4 AMR AF: 0.00300

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0494

Gnomad4 SAS AF: 0.0678

Gnomad4 FIN AF: 0.00171

Gnomad4 NFE AF: 0.00222

Gnomad4 OTH AF: 0.00600

Alfa AF: 0.000326 Hom.: 2

Bravo AF: 0.00768

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.36
Dann	Benign	0.75

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: rs210426; hg19: chrX-104934166;