rs210432

chrX-105703303-A-CchrX-105703303-A-T

Variant summary

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

The NM_017416.2(IL1RAPL2):c.773-14064A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 109,537 control chromosomes in the GnomAD database, including 9,826 homozygotes. There are 13,791 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 0.45 (9826 hom., 13791 hem., cov: 22)
• Consequence: IL1RAPL2 NM_017416.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.911

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 (AFR) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL1RAPL2	NM_017416.2	c.773-14064A>C		intron_variant		ENST00000372582.6
LOC105373303	XR_938493.3	n.662+13971T>G		intron_variant, non_coding_transcript_variant
IL1RAPL2	XM_011530905.3	c.401-14064A>C		intron_variant
LOC105373303	XR_007068300.1	n.4943T>G		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL1RAPL2	ENST00000372582.6	c.773-14064A>C		intron_variant		1	NM_017416.2	P1

Frequencies

GnomAD3 genomes AF: 0.453 AC: 49556 AN: 109486 Hom.: 9824 Cov.: 22 AF XY: 0.430 AC XY: 13740 AN XY: 31924

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.453 AC: 49609 AN: 109537 Hom.: 9826 Cov.: 22 AF XY: 0.431 AC XY: 13791 AN XY: 31985

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.411

Alfa AF: 0.336 Hom.: 8093

Bravo AF: 0.470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.20
Dann	Benign	0.41

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: rs210432; hg19: chrX-104947296;