chrX-118770110-T-A

Variant names:

• chrX-118770110-T-A
• rs2248857
• NM_001560.3:c.1009+3134T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001560.3(IL13RA1):​c.1009+3134T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 23)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: IL13RA1 NM_001560.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899
• Publications: 1 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL13RA1	NM_001560.3	c.1009+3134T>A		intron_variant	Intron 8 of 10	ENST00000371666.8	NP_001551.1
TMEM30BP1		n.118770110T>A		intragenic_variant
IL13RA1	XM_047442096.1	c.1009+3134T>A		intron_variant	Intron 8 of 10		XP_047298052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL13RA1	ENST00000371666.8	c.1009+3134T>A		intron_variant	Intron 8 of 10	1	NM_001560.3	ENSP00000360730.3
TMEM30BP1	ENST00000506969.1	n.315T>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
IL13RA1	ENST00000652600.1	c.1003+3134T>A		intron_variant	Intron 9 of 11			ENSP00000498980.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 148730 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 53454

African (AFR) AF: 0.00 AC: 0 AN: 4186

American (AMR) AF: 0.00 AC: 0 AN: 8636

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3367

East Asian (EAS) AF: 0.00 AC: 0 AN: 5919

South Asian (SAS) AF: 0.00 AC: 0 AN: 25404

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7196

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1645

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 84853

Other (OTH) AF: 0.00 AC: 0 AN: 7524

GnomAD4 genome Cov.: 23

Alfa AF: 0.00 Hom.: 513

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	3.0
DANN	Benign	0.89
PhyloP100		-0.90

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

Other links and lift over

dbSNP: rs2248857; hg19: chrX-117904073;