rs763737

chrX-154012856-G-AchrX-154012856-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001569.4(IRAK1):c.1931-178C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.68 (19574 hom., 22647 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: IRAK1 NM_001569.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

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]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd at 19583 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IRAK1	NM_001569.4	c.1931-178C>T		intron_variant		ENST00000369980.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IRAK1	ENST00000369980.8	c.1931-178C>T		intron_variant		1	NM_001569.4	P1

Frequencies

GnomAD3 genomes AF: 0.685 AC: 76359 AN: 111447 Hom.: 19583 Cov.: 24 AF XY: 0.673 AC XY: 22622 AN XY: 33637

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.960

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.651

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.645

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.685 AC: 76360 AN: 111499 Hom.: 19574 Cov.: 24 AF XY: 0.672 AC XY: 22647 AN XY: 33699

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.635

Alfa AF: 0.740 Hom.: 6046

Bravo AF: 0.660

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.2
Dann	Benign	0.38

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

Other links and lift over

dbSNP: rs763737; hg19: chrX-153278307; COSMIC: COSV64110753; COSMIC: COSV64110753;