X-105554323-G-T

Variant names:

• chrX-105554323-G-T
• rs1384360
• NM_017416.2:c.772+69936G>T

Variant summary

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

The NM_017416.2(IL1RAPL2):​c.772+69936G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 110,979 control chromosomes in the GnomAD database, including 10,061 homozygotes. There are 14,801 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 (10061 hom., 14801 hem., cov: 24)
• Consequence: IL1RAPL2 NM_017416.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1RAPL2	NM_017416.2	c.772+69936G>T		intron_variant	Intron 6 of 10	ENST00000372582.6	NP_059112.1
IL1RAPL2	XM_011530905.3	c.400+69936G>T		intron_variant	Intron 4 of 8		XP_011529207.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1RAPL2	ENST00000372582.6	c.772+69936G>T		intron_variant	Intron 6 of 10	1	NM_017416.2	ENSP00000361663.1

Frequencies

GnomAD3 genomes AF: 0.448 AC: 49708 AN: 110932 Hom.: 10051 Cov.: 24 AF XY: 0.443 AC XY: 14754 AN XY: 33296

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.448 AC: 49765 AN: 110979 Hom.: 10061 Cov.: 24 AF XY: 0.444 AC XY: 14801 AN XY: 33353

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.412

Alfa AF: 0.330 Hom.: 8934

Bravo AF: 0.488

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.021
DANN	Benign	0.12

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: rs1384360; hg19: chrX-104798316;