rs7061789

Positions:

• chrX-154015024-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001569.4(IRAK1):​c.1303-746C>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 (19332 hom., 21738 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: IRAK1 NM_001569.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IRAK1	NM_001569.4	c.1303-746C>T		intron_variant		ENST00000369980.8	NP_001560.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IRAK1	ENST00000369980.8	c.1303-746C>T		intron_variant		1	NM_001569.4	ENSP00000358997.3

Frequencies

GnomAD3 genomes AF: 0.680 AC: 75039 AN: 110339 Hom.: 19342 Cov.: 22 AF XY: 0.666 AC XY: 21711 AN XY: 32597

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.647

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.640

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: 0.680 AC: 75041 AN: 110391 Hom.: 19332 Cov.: 22 AF XY: 0.666 AC XY: 21738 AN XY: 32659

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.631

Alfa AF: 0.717 Hom.: 6457

Bravo AF: 0.655

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.51
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs7061789; hg19: chrX-153280475;