rs6646259

Positions:

• chrX-118770158-G-A
• chrX-118770158-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001560.3(IL13RA1):​c.1009+3182G>A 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 0.58 (13926 hom., 18690 hem., cov: 23)
  • Exomes 𝑓: 0.65 (21578 hom. 38158 hem.)
  • Failed GnomAD Quality Control
• Consequence: IL13RA1 NM_001560.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507

Genes affected

IL13RA1 (HGNC:5974): (interleukin 13 receptor subunit alpha 1) The protein encoded by this gene is a subunit of the interleukin 13 receptor. This subunit forms a receptor complex with IL4 receptor alpha, a subunit shared by IL13 and IL4 receptors. This subunit serves as a primary IL13-binding subunit of the IL13 receptor, and may also be a component of IL4 receptors. This protein has been shown to bind tyrosine kinase TYK2, and thus may mediate the signaling processes that lead to the activation of JAK1, STAT3 and STAT6 induced by IL13 and IL4. [provided by RefSeq, Jul 2008]

TMEM30BP1 (HGNC:55058): (TMEM30B pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAdExome4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL13RA1	NM_001560.3	c.1009+3182G>A		intron_variant		ENST00000371666.8
IL13RA1	XM_047442096.1	c.1009+3182G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL13RA1	ENST00000371666.8	c.1009+3182G>A		intron_variant		1	NM_001560.3	P1
TMEM30BP1	ENST00000506969.1	n.363G>A		non_coding_transcript_exon_variant	1/1
IL13RA1	ENST00000652600.1	c.1003+3182G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.579 AC: 63988 AN: 110607 Hom.: 13929 Cov.: 23 AF XY: 0.568 AC XY: 18672 AN XY: 32889

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.574

GnomAD4 exome AF: 0.650 AC: 103866 AN: 159908 Hom.: 21578 Cov.: 0 AF XY: 0.655 AC XY: 38158 AN XY: 58292

Gnomad4 AFR exome AF: 0.397

Gnomad4 AMR exome AF: 0.483

Gnomad4 ASJ exome AF: 0.705

Gnomad4 EAS exome AF: 0.555

Gnomad4 SAS exome AF: 0.642

Gnomad4 FIN exome AF: 0.660

Gnomad4 NFE exome AF: 0.690

Gnomad4 OTH exome AF: 0.657

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.578 AC: 63997 AN: 110661 Hom.: 13926 Cov.: 23 AF XY: 0.567 AC XY: 18690 AN XY: 32953

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.575

Alfa AF: 0.665 Hom.: 42467

Bravo AF: 0.557

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.3
DANN	Benign	0.64

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: rs6646259; hg19: chrX-117904121;