NM_001560.3:c.1009+3182G>A

Variant names:

• chrX-118770158-G-A
• rs6646259
• NM_001560.3:c.1009+3182G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
IL13RA1	NM_001560.3	c.1009+3182G>A		intron_variant	Intron 8 of 10	ENST00000371666.8	NP_001551.1
TMEM30BP1		n.118770158G>A		intragenic_variant
IL13RA1	XM_047442096.1	c.1009+3182G>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+3182G>A		intron_variant	Intron 8 of 10	1	NM_001560.3	ENSP00000360730.3
TMEM30BP1	ENST00000506969.1	n.363G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
IL13RA1	ENST00000652600.1	c.1003+3182G>A		intron_variant	Intron 9 of 11			ENSP00000498980.1

Frequencies

GnomAD3 genomes AF: 0.579 AC: 63988 AN: 110607 Hom.: 13929 Cov.: 23

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

African (AFR) AF: 0.397 AC: 1948 AN: 4903

American (AMR) AF: 0.483 AC: 5586 AN: 11565

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2678 AN: 3797

East Asian (EAS) AF: 0.555 AC: 3471 AN: 6250

South Asian (SAS) AF: 0.642 AC: 17622 AN: 27429

European-Finnish (FIN) AF: 0.660 AC: 4846 AN: 7341

Middle Eastern (MID) AF: 0.660 AC: 1147 AN: 1737

European-Non Finnish (NFE) AF: 0.690 AC: 61298 AN: 88867

Other (OTH) AF: 0.657 AC: 5270 AN: 8019

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

African (AFR) AF: 0.393 AC: 11977 AN: 30512

American (AMR) AF: 0.489 AC: 5164 AN: 10561

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 1835 AN: 2636

East Asian (EAS) AF: 0.571 AC: 1967 AN: 3444

South Asian (SAS) AF: 0.626 AC: 1643 AN: 2626

European-Finnish (FIN) AF: 0.641 AC: 3732 AN: 5825

Middle Eastern (MID) AF: 0.586 AC: 126 AN: 215

European-Non Finnish (NFE) AF: 0.687 AC: 36160 AN: 52665

Other (OTH) AF: 0.575 AC: 867 AN: 1509

Alfa AF: 0.636 Hom.: 59011

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
PhyloP100		-0.51
Mutation Taster		=100/0	polymorphism (auto)

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: rs6646259; hg19: chrX-117904121;