Variant X-154012438-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NM_001569.4(IRAK1):c.2080+91G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.68 ( 19454 hom., 22520 hem., cov: 23)

Exomes 𝑓: 0.76 ( 201966 hom. 205319 hem. )

Failed GnomAD Quality Control

Consequence

IRAK1
NM_001569.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.531

Variant links:

Genes affected

IRAK1 (HGNC:6112): (interleukin 1 receptor associated kinase 1) This gene encodes the interleukin-1 receptor-associated kinase 1, one of two putative serine/threonine kinases that become associated with the interleukin-1 receptor (IL1R) upon stimulation. This gene is partially responsible for IL1-induced upregulation of the transcription factor NF-kappa B. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

IRAK1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant X-154012438-C-T is Benign according to our data. Variant chrX-154012438-C-T is described in ClinVar as [Benign]. Clinvar id is 2688217.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IRAK1	NM_001569.4 link	c.2080+91G>A		intron_variant	Intron 13 of 13	ENST00000369980.8	NP_001560.2	P51617-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IRAK1	ENST00000369980.8 link	c.2080+91G>A		intron_variant	Intron 13 of 13	1	NM_001569.4	ENSP00000358997.3		P51617-1

Frequencies

GnomAD3 genomes

AF:

0.683

AC:

76065

AN:

111295

Hom.:

19463

Cov.:

AF XY:

0.671

AC XY:

22494

AN XY:

33525

show subpopulations

Gnomad AFR

AF:

0.569

Gnomad AMI

AF:

0.962

Gnomad AMR

AF:

0.544

Gnomad ASJ

AF:

0.738

Gnomad EAS

AF:

0.213

Gnomad SAS

AF:

0.358

Gnomad FIN

AF:

0.810

Gnomad MID

AF:

0.653

Gnomad NFE

AF:

0.806

Gnomad OTH

AF:

0.643

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.763

AC:

714940

AN:

936515

Hom.:

201966

AF XY:

0.757

AC XY:

205319

AN XY:

271325

show subpopulations

Gnomad4 AFR exome

AF:

0.582

Gnomad4 AMR exome

AF:

0.468

Gnomad4 ASJ exome

AF:

0.717

Gnomad4 EAS exome

AF:

0.229

Gnomad4 SAS exome

AF:

0.412

Gnomad4 FIN exome

AF:

0.823

Gnomad4 NFE exome

AF:

0.821

Gnomad4 OTH exome

AF:

0.707

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.683

AC:

76066

AN:

111350

Hom.:

19454

Cov.:

AF XY:

0.670

AC XY:

22520

AN XY:

33590

show subpopulations

Gnomad4 AFR

AF:

0.569

Gnomad4 AMR

AF:

0.543

Gnomad4 ASJ

AF:

0.738

Gnomad4 EAS

AF:

0.213

Gnomad4 SAS

AF:

0.360

Gnomad4 FIN

AF:

0.810

Gnomad4 NFE

AF:

0.806

Gnomad4 OTH

AF:

0.633

Alfa

AF:

0.753

Hom.:

7647

Bravo

AF:

0.658

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 34% of patients studied by a panel of primary immunodeficiencies. Number of patients: 32. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.3

DANN

Benign

0.74

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over