NM_014339.7:c.2160C>T

Variant names:

Variant summary

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

The NM_014339.7(IL17RA):c.2160C>T(p.Pro720Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 1,611,270 control chromosomes in the GnomAD database, including 46,797 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5467 hom., cov: 34)

Exomes 𝑓: 0.23 ( 41330 hom. )

Consequence

IL17RA
NM_014339.7 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6O:1

Conservation

PhyloP100: -2.91

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=-0.71).

BP6

Variant 22-17109379-C-T is Benign according to our data. Variant chr22-17109379-C-T is described in ClinVar as [Benign]. Clinvar id is 340608.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-17109379-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-2.91 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17RA	NM_014339.7 link	c.2160C>T	p.Pro720Pro	synonymous_variant	Exon 13 of 13	ENST00000319363.11	NP_055154.3	Q96F46-1
IL17RA	NM_001289905.2 link	c.2058C>T	p.Pro686Pro	synonymous_variant	Exon 12 of 12		NP_001276834.1	Q96F46-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL17RA	ENST00000319363.11 link	c.2160C>T	p.Pro720Pro	synonymous_variant	Exon 13 of 13	1	NM_014339.7	ENSP00000320936.6		Q96F46-1
IL17RA	ENST00000612619.2 link	c.2058C>T	p.Pro686Pro	synonymous_variant	Exon 12 of 12	5		ENSP00000479970.1		Q96F46-2

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39893

AN:

152072

Hom.:

5458

Cov.:

show subpopulations

Gnomad AFR

AF:

0.338

Gnomad AMI

AF:

0.208

Gnomad AMR

AF:

0.258

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.0838

Gnomad SAS

AF:

0.183

Gnomad FIN

AF:

0.222

Gnomad MID

AF:

0.309

Gnomad NFE

AF:

0.244

Gnomad OTH

AF:

0.268

GnomAD3 exomes

AF:

0.228

AC:

55500

AN:

243612

Hom.:

6657

AF XY:

0.224

AC XY:

29815

AN XY:

132968

show subpopulations

Gnomad AFR exome

AF:

0.338

Gnomad AMR exome

AF:

0.248

Gnomad ASJ exome

AF:

0.255

Gnomad EAS exome

AF:

0.0756

Gnomad SAS exome

AF:

0.185

Gnomad FIN exome

AF:

0.225

Gnomad NFE exome

AF:

0.241

Gnomad OTH exome

AF:

0.230

GnomAD4 exome

AF:

0.234

AC:

341853

AN:

1459080

Hom.:

41330

Cov.:

AF XY:

0.232

AC XY:

168587

AN XY:

725756

show subpopulations

Gnomad4 AFR exome

AF:

0.343

Gnomad4 AMR exome

AF:

0.251

Gnomad4 ASJ exome

AF:

0.255

Gnomad4 EAS exome

AF:

0.0825

Gnomad4 SAS exome

AF:

0.183

Gnomad4 FIN exome

AF:

0.221

Gnomad4 NFE exome

AF:

0.240

Gnomad4 OTH exome

AF:

0.234

GnomAD4 genome

AF:

0.262

AC:

39931

AN:

152190

Hom.:

5467

Cov.:

AF XY:

0.259

AC XY:

19256

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.338

Gnomad4 AMR

AF:

0.258

Gnomad4 ASJ

AF:

0.251

Gnomad4 EAS

AF:

0.0828

Gnomad4 SAS

AF:

0.182

Gnomad4 FIN

AF:

0.222

Gnomad4 NFE

AF:

0.244

Gnomad4 OTH

AF:

0.267

Alfa

AF:

0.211

Hom.:

1140

Bravo

AF:

0.267

Asia WGS

AF:

0.165

AC:

574

AN:

3478

EpiCase

AF:

0.244

EpiControl

AF:

0.246

ClinVar

Significance: Benign

Submissions summary: Benign:6Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2Other:1

May 17, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

GenomeConnect, ClinGen

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -

not specified

Benign:2

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 42% of patients studied by a panel of primary immunodeficiencies. Number of patients: 40. Only high quality variants are reported. -

Familial Candidiasis, Recessive

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Immunodeficiency 51

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.20

DANN

Benign

0.70

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