Variant rs3804060 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.2490C>T(p.Pro830Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00601 in 1,589,426 control chromosomes in the GnomAD database, including 257 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0092 ( 46 hom., cov: 34)

Exomes 𝑓: 0.0057 ( 211 hom. )

Consequence

IL17RA
NM_014339.7 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -3.06

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 22-17109709-C-T is Benign according to our data. Variant chr22-17109709-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 340613.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.06 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL17RA	NM_014339.7 link	c.2490C>T	p.Pro830Pro	synonymous_variant	13/13	ENST00000319363.11	NP_055154.3	Q96F46-1
IL17RA	NM_001289905.2 link	c.2388C>T	p.Pro796Pro	synonymous_variant	12/12		NP_001276834.1	Q96F46-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL17RA	ENST00000319363.11 link	c.2490C>T	p.Pro830Pro	synonymous_variant	13/13	1	NM_014339.7	ENSP00000320936.6		Q96F46-1
IL17RA	ENST00000612619.2 link	c.2388C>T	p.Pro796Pro	synonymous_variant	12/12	5		ENSP00000479970.1		Q96F46-2

Frequencies

GnomAD3 genomes

AF:

0.00916

AC:

1394

AN:

152172

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00485

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0320

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.0913

Gnomad SAS

AF:

0.0244

Gnomad FIN

AF:

0.0000941

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00123

Gnomad OTH

AF:

0.0120

GnomAD3 exomes

AF:

0.0154

AC:

3084

AN:

200726

Hom.:

AF XY:

0.0146

AC XY:

1597

AN XY:

109426

show subpopulations

Gnomad AFR exome

AF:

0.00435

Gnomad AMR exome

AF:

0.0304

Gnomad ASJ exome

AF:

0.00111

Gnomad EAS exome

AF:

0.0911

Gnomad SAS exome

AF:

0.0209

Gnomad FIN exome

AF:

0.000519

Gnomad NFE exome

AF:

0.00160

Gnomad OTH exome

AF:

0.00785

GnomAD4 exome

AF:

0.00567

AC:

8155

AN:

1437136

Hom.:

211

Cov.:

AF XY:

0.00594

AC XY:

4236

AN XY:

712678

show subpopulations

Gnomad4 AFR exome

AF:

0.00558

Gnomad4 AMR exome

AF:

0.0304

Gnomad4 ASJ exome

AF:

0.000586

Gnomad4 EAS exome

AF:

0.0809

Gnomad4 SAS exome

AF:

0.0206

Gnomad4 FIN exome

AF:

0.000378

Gnomad4 NFE exome

AF:

0.00114

Gnomad4 OTH exome

AF:

0.00861

GnomAD4 genome

AF:

0.00918

AC:

1398

AN:

152290

Hom.:

Cov.:

AF XY:

0.0105

AC XY:

783

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.00488

Gnomad4 AMR

AF:

0.0322

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.0913

Gnomad4 SAS

AF:

0.0242

Gnomad4 FIN

AF:

0.0000941

Gnomad4 NFE

AF:

0.00123

Gnomad4 OTH

AF:

0.0118

Alfa

AF:

0.00307

Hom.:

Bravo

AF:

0.0107

Asia WGS

AF:

0.0400

AC:

139

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Familial Candidiasis, Recessive

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Likely 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 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.11

DANN

Benign

0.62

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