X-115014860-G-T

Position:

• chrX-115014860-G-T

Variant summary

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

The NM_000640.3(IL13RA2):​c.247-286C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 110,900 control chromosomes in the GnomAD database, including 942 homozygotes. There are 4,510 hemizygotes in GnomAD. 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 0.15 (942 hom., 4510 hem., cov: 22)
• Consequence: IL13RA2 NM_000640.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.650

Genes affected

IL13RA2 (HGNC:5975): (interleukin 13 receptor subunit alpha 2) The protein encoded by this gene is closely related to Il13RA1, a subuint of the interleukin 13 receptor complex. This protein binds IL13 with high affinity, but lacks cytoplasmic domain, and does not appear to function as a signal mediator. It is reported to play a role in the internalization of IL13. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL13RA2	NM_000640.3	c.247-286C>A		intron_variant		ENST00000243213.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL13RA2	ENST00000243213.2	c.247-286C>A		intron_variant		1	NM_000640.3	P1
IL13RA2	ENST00000371936.5	c.247-286C>A		intron_variant		5		P1
IL13RA2	ENST00000468224.1	n.551-286C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.147 AC: 16293 AN: 110850 Hom.: 940 Cov.: 22 AF XY: 0.136 AC XY: 4492 AN XY: 33118

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.0836

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.00536

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.147 AC: 16312 AN: 110900 Hom.: 942 Cov.: 22 AF XY: 0.136 AC XY: 4510 AN XY: 33178

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.0835

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.00538

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.115

Alfa AF: 0.147 Hom.: 2116

Bravo AF: 0.148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.060
DANN	Benign	0.33

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: rs10521698; hg19: chrX-114249423;