Variant rs455863 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001193380.2(IL17RE):c.1417G>A(p.Gly473Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 1,613,342 control chromosomes in the GnomAD database, including 213,584 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.48 ( 18300 hom., cov: 32)

Exomes 𝑓: 0.51 ( 195284 hom. )

Consequence

IL17RE
NM_001193380.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.33

Variant links:

Genes affected

IL17RE (HGNC:18439): (interleukin 17 receptor E) This gene encodes a transmembrane protein that functions as the receptor for interleukin-17C. The encoded protein signals to downstream components of the mitogen activated protein kinase (MAPK) pathway. Activity of this protein is important in the immune response to bacterial pathogens. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Sep 2013]

IL17RE links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=5.691617E-6).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL17RE	NM_153480.2 link	c.1344G>A	p.Pro448Pro	synonymous_variant	14/16	ENST00000383814.8	NP_705613.1	Q8NFR9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL17RE	ENST00000383814.8 link	c.1344G>A	p.Pro448Pro	synonymous_variant	14/16	1	NM_153480.2	ENSP00000373325.3		Q8NFR9-1

Frequencies

GnomAD3 genomes

AF:

0.481

AC:

73002

AN:

151926

Hom.:

18287

Cov.:

show subpopulations

Gnomad AFR

AF:

0.412

Gnomad AMI

AF:

0.611

Gnomad AMR

AF:

0.485

Gnomad ASJ

AF:

0.456

Gnomad EAS

AF:

0.0869

Gnomad SAS

AF:

0.335

Gnomad FIN

AF:

0.588

Gnomad MID

AF:

0.563

Gnomad NFE

AF:

0.544

Gnomad OTH

AF:

0.483

GnomAD3 exomes

AF:

0.460

AC:

115517

AN:

251132

Hom.:

28939

AF XY:

0.462

AC XY:

62719

AN XY:

135738

show subpopulations

Gnomad AFR exome

AF:

0.403

Gnomad AMR exome

AF:

0.432

Gnomad ASJ exome

AF:

0.459

Gnomad EAS exome

AF:

0.0811

Gnomad SAS exome

AF:

0.349

Gnomad FIN exome

AF:

0.589

Gnomad NFE exome

AF:

0.541

Gnomad OTH exome

AF:

0.496

GnomAD4 exome

AF:

0.508

AC:

742812

AN:

1461300

Hom.:

195284

Cov.:

AF XY:

0.505

AC XY:

367161

AN XY:

726962

show subpopulations

Gnomad4 AFR exome

AF:

0.404

Gnomad4 AMR exome

AF:

0.437

Gnomad4 ASJ exome

AF:

0.458

Gnomad4 EAS exome

AF:

0.0818

Gnomad4 SAS exome

AF:

0.354

Gnomad4 FIN exome

AF:

0.579

Gnomad4 NFE exome

AF:

0.540

Gnomad4 OTH exome

AF:

0.492

GnomAD4 genome

AF:

0.480

AC:

73047

AN:

152042

Hom.:

18300

Cov.:

AF XY:

0.478

AC XY:

35502

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.412

Gnomad4 AMR

AF:

0.485

Gnomad4 ASJ

AF:

0.456

Gnomad4 EAS

AF:

0.0864

Gnomad4 SAS

AF:

0.336

Gnomad4 FIN

AF:

0.588

Gnomad4 NFE

AF:

0.544

Gnomad4 OTH

AF:

0.488

Alfa

AF:

0.522

Hom.:

45094

Bravo

AF:

0.470

TwinsUK

AF:

0.538

AC:

1995

ALSPAC

AF:

0.525

AC:

2022

ESP6500AA

AF:

0.415

AC:

1829

ESP6500EA

AF:

0.532

AC:

4579

ExAC

AF:

0.461

AC:

55926

Asia WGS

AF:

0.288

AC:

996

AN:

3478

EpiCase

AF:

0.538

EpiControl

AF:

0.540

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.44

CADD

Benign

0.022

DANN

Benign

0.81

Eigen

Benign

-2.2

Eigen_PC

Benign

-2.3

FATHMM_MKL

Benign

0.012

LIST_S2

Benign

0.26

MetaRNN

Benign

0.0000057

MetaSVM

Benign

-0.99

PROVEAN

Benign

0.66

REVEL

Benign

0.064

Sift

Pathogenic

0.0

Sift4G

Benign

0.29

Polyphen

0.0

Vest4

0.28

MutPred

0.29

Gain of helix (P = 0.0425);

ClinPred

0.020

GERP RS

-9.9

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over