Variant rs879576 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_014339.7(IL17RA):c.1137G>A(p.Lys379=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,613,960 control chromosomes in the GnomAD database, including 12,799 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 1892 hom., cov: 33)

Exomes 𝑓: 0.12 ( 10907 hom. )

Consequence

IL17RA
NM_014339.7 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.31

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 -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BP6

Variant 22-17108356-G-A is Benign according to our data. Variant chr22-17108356-G-A is described in ClinVar as [Benign]. Clinvar id is 340592.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-17108356-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=1.31 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL17RA	NM_014339.7 linkuse as main transcript	c.1137G>A	p.Lys379=	synonymous_variant	13/13	ENST00000319363.11
IL17RA	NM_001289905.2 linkuse as main transcript	c.1035G>A	p.Lys345=	synonymous_variant	12/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17RA	ENST00000319363.11 linkuse as main transcript	c.1137G>A	p.Lys379=	synonymous_variant	13/13	1	NM_014339.7	P2	Q96F46-1
IL17RA	ENST00000612619.2 linkuse as main transcript	c.1035G>A	p.Lys345=	synonymous_variant	12/12	5		A2	Q96F46-2

Frequencies

GnomAD3 genomes

AF:

0.146

AC:

22154

AN:

152056

Hom.:

1890

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.0636

Gnomad AMR

AF:

0.121

Gnomad ASJ

AF:

0.228

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.106

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.116

Gnomad OTH

AF:

0.151

GnomAD3 exomes

AF:

0.114

AC:

28544

AN:

251174

Hom.:

2027

AF XY:

0.115

AC XY:

15649

AN XY:

135786

show subpopulations

Gnomad AFR exome

AF:

0.236

Gnomad AMR exome

AF:

0.0759

Gnomad ASJ exome

AF:

0.228

Gnomad EAS exome

AF:

0.000598

Gnomad SAS exome

AF:

0.109

Gnomad FIN exome

AF:

0.111

Gnomad NFE exome

AF:

0.117

Gnomad OTH exome

AF:

0.120

GnomAD4 exome

AF:

0.116

AC:

169645

AN:

1461784

Hom.:

10907

Cov.:

AF XY:

0.117

AC XY:

84805

AN XY:

727198

show subpopulations

Gnomad4 AFR exome

AF:

0.232

Gnomad4 AMR exome

AF:

0.0798

Gnomad4 ASJ exome

AF:

0.228

Gnomad4 EAS exome

AF:

0.000327

Gnomad4 SAS exome

AF:

0.111

Gnomad4 FIN exome

AF:

0.113

Gnomad4 NFE exome

AF:

0.115

Gnomad4 OTH exome

AF:

0.127

GnomAD4 genome

AF:

0.146

AC:

22171

AN:

152176

Hom.:

1892

Cov.:

AF XY:

0.144

AC XY:

10679

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.229

Gnomad4 AMR

AF:

0.120

Gnomad4 ASJ

AF:

0.228

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.106

Gnomad4 FIN

AF:

0.113

Gnomad4 NFE

AF:

0.116

Gnomad4 OTH

AF:

0.150

Alfa

AF:

0.118

Hom.:

1261

Bravo

AF:

0.150

Asia WGS

AF:

0.0580

AC:

202

AN:

3478

EpiCase

AF:

0.129

EpiControl

AF:

0.126

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 26% of patients studied by a panel of primary immunodeficiencies. Number of patients: 25. Only high quality variants are reported. -

Familial Candidiasis, Recessive

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Immunodeficiency 51

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

6.9

DANN

Benign

0.60

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