Variant rs2229151 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_014339.7(IL17RA):c.1188G>A(p.Leu396=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0281 in 1,614,048 control chromosomes in the GnomAD database, including 4,307 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.030 ( 405 hom., cov: 34)

Exomes 𝑓: 0.028 ( 3902 hom. )

Consequence

IL17RA
NM_014339.7 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.36

Variant links:

Genes affected

IL17RA (HGNC:5985): (interleukin 17 receptor A) Interleukin 17A (IL17A) is a proinflammatory cytokine secreted by activated T-lymphocytes. It is a potent inducer of the maturation of CD34-positive hematopoietic precursors into neutrophils. The transmembrane protein encoded by this gene (interleukin 17A receptor; IL17RA) is a ubiquitous type I membrane glycoprotein that binds with low affinity to interleukin 17A. Interleukin 17A and its receptor play a pathogenic role in many inflammatory and autoimmune diseases such as rheumatoid arthritis. Like other cytokine receptors, this receptor likely has a multimeric structure. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2014]

IL17RA links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 22-17108407-G-A is Benign according to our data. Variant chr22-17108407-G-A is described in ClinVar as [Benign]. Clinvar id is 340594.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.36 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL17RA	NM_014339.7 linkuse as main transcript	c.1188G>A	p.Leu396=	synonymous_variant	13/13	ENST00000319363.11	NP_055154.3
IL17RA	NM_001289905.2 linkuse as main transcript	c.1086G>A	p.Leu362=	synonymous_variant	12/12		NP_001276834.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL17RA	ENST00000319363.11 linkuse as main transcript	c.1188G>A	p.Leu396=	synonymous_variant	13/13	1	NM_014339.7	ENSP00000320936	P2	Q96F46-1
IL17RA	ENST00000612619.2 linkuse as main transcript	c.1086G>A	p.Leu362=	synonymous_variant	12/12	5		ENSP00000479970	A2	Q96F46-2

Frequencies

GnomAD3 genomes

AF:

0.0295

AC:

4492

AN:

152196

Hom.:

406

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00449

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0784

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.301

Gnomad SAS

AF:

0.146

Gnomad FIN

AF:

0.0389

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00454

Gnomad OTH

AF:

0.0315

GnomAD3 exomes

AF:

0.0757

AC:

19011

AN:

251140

Hom.:

2086

AF XY:

0.0722

AC XY:

9800

AN XY:

135792

show subpopulations

Gnomad AFR exome

AF:

0.00511

Gnomad AMR exome

AF:

0.197

Gnomad ASJ exome

AF:

0.0162

Gnomad EAS exome

AF:

0.313

Gnomad SAS exome

AF:

0.144

Gnomad FIN exome

AF:

0.0396

Gnomad NFE exome

AF:

0.00549

Gnomad OTH exome

AF:

0.0545

GnomAD4 exome

AF:

0.0279

AC:

40839

AN:

1461734

Hom.:

3902

Cov.:

AF XY:

0.0304

AC XY:

22117

AN XY:

727172

show subpopulations

Gnomad4 AFR exome

AF:

0.00299

Gnomad4 AMR exome

AF:

0.183

Gnomad4 ASJ exome

AF:

0.0157

Gnomad4 EAS exome

AF:

0.290

Gnomad4 SAS exome

AF:

0.139

Gnomad4 FIN exome

AF:

0.0412

Gnomad4 NFE exome

AF:

0.00354

Gnomad4 OTH exome

AF:

0.0404

GnomAD4 genome

AF:

0.0296

AC:

4501

AN:

152314

Hom.:

405

Cov.:

AF XY:

0.0350

AC XY:

2604

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.00447

Gnomad4 AMR

AF:

0.0785

Gnomad4 ASJ

AF:

0.0150

Gnomad4 EAS

AF:

0.301

Gnomad4 SAS

AF:

0.146

Gnomad4 FIN

AF:

0.0389

Gnomad4 NFE

AF:

0.00454

Gnomad4 OTH

AF:

0.0345

Alfa

AF:

0.0221

Hom.:

165

Bravo

AF:

0.0342

Asia WGS

AF:

0.209

AC:

727

AN:

3478

EpiCase

AF:

0.00333

EpiControl

AF:

0.00350

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Familial Candidiasis, Recessive

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Immunodeficiency 51

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 30, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.27

DANN

Benign

0.79

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