rs5962575

Variant names:

• chrX-105737511-T-C
• rs5962575
• NM_017416.2:c.903-3035T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017416.2(IL1RAPL2):​c.903-3035T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 110,778 control chromosomes in the GnomAD database, including 844 homozygotes. There are 4,213 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 0.13 (844 hom., 4213 hem., cov: 22)
• Consequence: IL1RAPL2 NM_017416.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 2 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]

LOC105373303 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1RAPL2	NM_017416.2	c.903-3035T>C		intron_variant	Intron 7 of 10	ENST00000372582.6	NP_059112.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1RAPL2	ENST00000372582.6	c.903-3035T>C		intron_variant	Intron 7 of 10	1	NM_017416.2	ENSP00000361663.1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 14867 AN: 110724 Hom.: 848 Cov.: 22

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.0899

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.0743

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0912

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.134 AC: 14867 AN: 110778 Hom.: 844 Cov.: 22 AF XY: 0.127 AC XY: 4213 AN XY: 33088

African (AFR) AF: 0.212 AC: 6457 AN: 30430

American (AMR) AF: 0.0898 AC: 937 AN: 10429

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 401 AN: 2634

East Asian (EAS) AF: 0.218 AC: 749 AN: 3437

South Asian (SAS) AF: 0.249 AC: 645 AN: 2588

European-Finnish (FIN) AF: 0.0743 AC: 443 AN: 5964

Middle Eastern (MID) AF: 0.172 AC: 37 AN: 215

European-Non Finnish (NFE) AF: 0.0912 AC: 4825 AN: 52900

Other (OTH) AF: 0.129 AC: 194 AN: 1507

Alfa AF: 0.111 Hom.: 9957

Bravo AF: 0.141

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	7.8
DANN	Benign	0.82
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs5962575; hg19: chrX-104981504;