NM_017416.2:c.773-25574G>T

Variant names:

• chrX-105691793-G-T
• rs210427
• NM_017416.2:c.773-25574G>T

Variant summary

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

The NM_017416.2(IL1RAPL2):​c.773-25574G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 110,284 control chromosomes in the GnomAD database, including 8,651 homozygotes. There are 13,712 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 0.44 (8651 hom., 13712 hem., cov: 23)
• Consequence: IL1RAPL2 NM_017416.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1RAPL2	NM_017416.2	c.773-25574G>T		intron_variant	Intron 6 of 10	ENST00000372582.6	NP_059112.1
IL1RAPL2	XM_011530905.3	c.401-25574G>T		intron_variant	Intron 4 of 8		XP_011529207.1
LOC105373303	XR_938493.3	n.662+25481C>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1RAPL2	ENST00000372582.6	c.773-25574G>T		intron_variant	Intron 6 of 10	1	NM_017416.2	ENSP00000361663.1

Frequencies

GnomAD3 genomes AF: 0.440 AC: 48501 AN: 110232 Hom.: 8650 Cov.: 23

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.440 AC: 48537 AN: 110284 Hom.: 8651 Cov.: 23 AF XY: 0.421 AC XY: 13712 AN XY: 32590

African (AFR) AF: 0.671 AC: 20351 AN: 30313

American (AMR) AF: 0.291 AC: 3010 AN: 10342

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1220 AN: 2632

East Asian (EAS) AF: 0.178 AC: 619 AN: 3484

South Asian (SAS) AF: 0.344 AC: 917 AN: 2663

European-Finnish (FIN) AF: 0.306 AC: 1760 AN: 5758

Middle Eastern (MID) AF: 0.401 AC: 85 AN: 212

European-Non Finnish (NFE) AF: 0.372 AC: 19598 AN: 52702

Other (OTH) AF: 0.396 AC: 596 AN: 1506

Alfa AF: 0.227 Hom.: 1058

Bravo AF: 0.447

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.71
PhyloP100		0.063
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs210427; hg19: chrX-104935786;