Variant X-105554323-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.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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.41

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:

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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=-0.99).

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/exons	MANE	Protein	UniProt
IL1RAPL2	NM_017416.2 linkuse as main transcript	c.772+69936G>T		intron_variant		ENST00000372582.6	NP_059112.1
IL1RAPL2	XM_011530905.3 linkuse as main transcript	c.400+69936G>T		intron_variant			XP_011529207.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL1RAPL2	ENST00000372582.6 linkuse as main transcript	c.772+69936G>T		intron_variant		1	NM_017416.2	ENSP00000361663	P1

Frequencies

GnomAD3 genomes

AF:

0.448

AC:

49708

AN:

110932

Hom.:

10051

Cov.:

AF XY:

0.443

AC XY:

14754

AN XY:

33296

show subpopulations

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.:

AF XY:

0.444

AC XY:

14801

AN XY:

33353

show subpopulations

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

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