NM_017416.2:c.1193-3016C>T

Variant names:

• chrX-105752161-C-T
• rs9887672
• NM_017416.2:c.1193-3016C>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.1193-3016C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 110,936 control chromosomes in the GnomAD database, including 747 homozygotes. There are 4,015 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 (747 hom., 4015 hem., cov: 23)
• Consequence: IL1RAPL2 NM_017416.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017416.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1RAPL2	NM_017416.2	MANE Select	c.1193-3016C>T		intron	N/A	NP_059112.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL1RAPL2	ENST00000372582.6	TSL:1 MANE Select	c.1193-3016C>T		intron	N/A	ENSP00000361663.1
	IL1RAPL2	ENST00000485671.1	TSL:5	n.188-3016C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.125 AC: 13876 AN: 110882 Hom.: 747 Cov.: 23

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.0802

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.0657

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.125 AC: 13885 AN: 110936 Hom.: 747 Cov.: 23 AF XY: 0.121 AC XY: 4015 AN XY: 33216

African (AFR) AF: 0.196 AC: 5969 AN: 30485

American (AMR) AF: 0.0802 AC: 836 AN: 10425

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 401 AN: 2633

East Asian (EAS) AF: 0.186 AC: 646 AN: 3482

South Asian (SAS) AF: 0.288 AC: 756 AN: 2621

European-Finnish (FIN) AF: 0.0657 AC: 391 AN: 5954

Middle Eastern (MID) AF: 0.146 AC: 31 AN: 212

European-Non Finnish (NFE) AF: 0.0849 AC: 4493 AN: 52923

Other (OTH) AF: 0.116 AC: 177 AN: 1520

Alfa AF: 0.112 Hom.: 3110

Bravo AF: 0.130

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.2
DANN	Benign	0.73
PhyloP100		0.46
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: rs9887672; hg19: chrX-104996155;