Variant X-118758117-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_001560.3(IL13RA1):c.551G>A(p.Gly184Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000145 in 1,168,277 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 48 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000054 ( 0 hom., 2 hem., cov: 22)

Exomes 𝑓: 0.00015 ( 0 hom. 46 hem. )

Consequence

IL13RA1
NM_001560.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.257

Variant links:

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]

IL13RA1 links:

IL13RA1 (HGNC:):

IL13RA1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant X-118758117-G-A is Benign according to our data. Variant chrX-118758117-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 754602.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL13RA1	NM_001560.3 linkuse as main transcript	c.551G>A	p.Gly184Asp	missense_variant	5/11	ENST00000371666.8	NP_001551.1	P78552-1
IL13RA1	XM_047442096.1 linkuse as main transcript	c.551G>A	p.Gly184Asp	missense_variant	5/11		XP_047298052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
IL13RA1	ENST00000371666.8 linkuse as main transcript	c.551G>A	p.Gly184Asp	missense_variant	5/11	1	NM_001560.3	ENSP00000360730.3	P78552-1
IL13RA1	ENST00000371642.1 linkuse as main transcript	c.551G>A	p.Gly184Asp	missense_variant	5/6	1		ENSP00000360705.1	P78552-2
IL13RA1	ENST00000652600.1 linkuse as main transcript	c.545G>A	p.Gly182Asp	missense_variant	6/12			ENSP00000498980.1	A0A494C1C4
IL13RA1	ENST00000481868.1 linkuse as main transcript	n.139G>A		non_coding_transcript_exon_variant	2/6	3

Frequencies

GnomAD3 genomes

AF:

0.0000536

AC:

AN:

111940

Hom.:

Cov.:

AF XY:

0.0000587

AC XY:

AN XY:

34096

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000166

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000939

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000350

AC:

AN:

183075

Hom.:

AF XY:

0.000311

AC XY:

AN XY:

67535

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000250

Gnomad NFE exome

AF:

0.000709

Gnomad OTH exome

AF:

0.000442

GnomAD4 exome

AF:

0.000154

AC:

163

AN:

1056337

Hom.:

Cov.:

AF XY:

0.000140

AC XY:

AN XY:

328123

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.000324

Gnomad4 NFE exome

AF:

0.000167

Gnomad4 OTH exome

AF:

0.000338

GnomAD4 genome

AF:

0.0000536

AC:

AN:

111940

Hom.:

Cov.:

AF XY:

0.0000587

AC XY:

AN XY:

34096

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000166

Gnomad4 NFE

AF:

0.0000939

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.0000907

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000346

AC:

ExAC

AF:

0.000626

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 13, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.35

BayesDel_addAF

Benign

-0.15

BayesDel_noAF

Uncertain

-0.080

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Pathogenic

0.89

D;.

FATHMM_MKL

Benign

0.23

LIST_S2

Benign

0.58

T;T

M_CAP

Pathogenic

0.73

MetaRNN

Uncertain

0.58

D;D

MetaSVM

Uncertain

0.54

MutationAssessor

Uncertain

2.4

M;M

PrimateAI

Benign

0.39

PROVEAN

Uncertain

-4.3

D;D

REVEL

Uncertain

0.42

Sift

Uncertain

0.0050

D;D

Sift4G

Uncertain

0.012

D;D

Polyphen

1.0

D;.

Vest4

0.51

MVP

0.92

MPC

0.71

ClinPred

0.22

GERP RS

-1.2

Varity_R

0.81

gMVP

0.84

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over