Variant X-105708824-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017416.2(IL1RAPL2):c.773-8543G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 110,745 control chromosomes in the GnomAD database, including 2,768 homozygotes. There are 7,647 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 0.22 ( 2768 hom., 7647 hem., cov: 23)

Consequence

IL1RAPL2
NM_017416.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.37

Variant links:

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]

IL1RAPL2 links:

LOC105373303 (HGNC:):

LOC105373303 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
IL1RAPL2	NM_017416.2 linkuse as main transcript	c.773-8543G>T	intron_variant	ENST00000372582.6
LOC105373303	XR_938493.3 linkuse as main transcript	n.662+8450C>A	intron_variant, non_coding_transcript_variant
IL1RAPL2	XM_011530905.3 linkuse as main transcript	c.401-8543G>T	intron_variant
LOC105373303	XR_007068300.1 linkuse as main transcript	n.890-1468C>A	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL1RAPL2	ENST00000372582.6 linkuse as main transcript	c.773-8543G>T		intron_variant		1	NM_017416.2	P1

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

24749

AN:

110693

Hom.:

2763

Cov.:

AF XY:

0.232

AC XY:

7643

AN XY:

33013

show subpopulations

Gnomad AFR

AF:

0.0396

Gnomad AMI

AF:

0.232

Gnomad AMR

AF:

0.440

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.631

Gnomad SAS

AF:

0.281

Gnomad FIN

AF:

0.371

Gnomad MID

AF:

0.0766

Gnomad NFE

AF:

0.244

Gnomad OTH

AF:

0.249

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

GnomAD4 genome

AF:

0.223

AC:

24750

AN:

110745

Hom.:

2768

Cov.:

AF XY:

0.231

AC XY:

7647

AN XY:

33075

show subpopulations

Gnomad4 AFR

AF:

0.0395

Gnomad4 AMR

AF:

0.441

Gnomad4 ASJ

AF:

0.177

Gnomad4 EAS

AF:

0.633

Gnomad4 SAS

AF:

0.282

Gnomad4 FIN

AF:

0.371

Gnomad4 NFE

AF:

0.244

Gnomad4 OTH

AF:

0.245

Alfa

AF:

0.252

Hom.:

13694

Bravo

AF:

0.230

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

8.5

DANN

Benign

0.45

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over