chrX-118770345-C-T

Variant names:

• chrX-118770345-C-T
• rs1209600749
• NM_001560.3:c.1009+3369C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001560.3(IL13RA1):​c.1009+3369C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000612 in 359,713 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.000035 (0 hom., 0 hem., cov: 24)
  • Exomes 𝑓: 0.000073 (0 hom. 5 hem.)
• Consequence: IL13RA1 NM_001560.3 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.109
• Publications: 0 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant X-118770345-C-T is Benign according to our data. Variant chrX-118770345-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2661275.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Hemizygotes in GnomAdExome4 at 5 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001560.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL13RA1	NM_001560.3	MANE Select	c.1009+3369C>T		intron	N/A	NP_001551.1	P78552-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL13RA1	ENST00000371666.8	TSL:1 MANE Select	c.1009+3369C>T		intron	N/A	ENSP00000360730.3	P78552-1
	IL13RA1	ENST00000965042.1		c.1150+3369C>T		intron	N/A	ENSP00000635101.1
	IL13RA1	ENST00000865793.1		c.1009+3369C>T		intron	N/A	ENSP00000535852.1

Frequencies

GnomAD3 genomes AF: 0.0000355 AC: 4 AN: 112695 Hom.: 0 Cov.: 24

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000929

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000563

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000108 AC: 11 AN: 102162 AF XY: 0.0000811

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000155

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000197

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000729 AC: 18 AN: 247018 Hom.: 0 Cov.: 0 AF XY: 0.0000542 AC XY: 5 AN XY: 92268

African (AFR) AF: 0.00 AC: 0 AN: 7785

American (AMR) AF: 0.000134 AC: 3 AN: 22368

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9001

East Asian (EAS) AF: 0.00 AC: 0 AN: 8843

South Asian (SAS) AF: 0.00 AC: 0 AN: 36549

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12822

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2207

European-Non Finnish (NFE) AF: 0.000104 AC: 14 AN: 134834

Other (OTH) AF: 0.0000793 AC: 1 AN: 12609

GnomAD4 genome AF: 0.0000355 AC: 4 AN: 112695 Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0 AN XY: 34845

African (AFR) AF: 0.00 AC: 0 AN: 31025

American (AMR) AF: 0.0000929 AC: 1 AN: 10770

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2650

East Asian (EAS) AF: 0.00 AC: 0 AN: 3572

South Asian (SAS) AF: 0.00 AC: 0 AN: 2759

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6199

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 240

European-Non Finnish (NFE) AF: 0.0000563 AC: 3 AN: 53271

Other (OTH) AF: 0.00 AC: 0 AN: 1523

Alfa AF: 0.000174 Hom.: 0

Bravo AF: 0.0000529

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.71
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism

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: rs1209600749; hg19: chrX-117904308;