rs279572

Positions:

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_153480.2(IL17RE):ā€‹c.960A>Gā€‹(p.Thr320=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 1,613,796 control chromosomes in the GnomAD database, including 226,236 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.54 ( 23299 hom., cov: 32)
Exomes š‘“: 0.52 ( 202937 hom. )

Consequence

IL17RE
NM_153480.2 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.52
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP7
Synonymous conserved (PhyloP=-1.52 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL17RENM_153480.2 linkuse as main transcriptc.960A>G p.Thr320= synonymous_variant 9/16 ENST00000383814.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL17REENST00000383814.8 linkuse as main transcriptc.960A>G p.Thr320= synonymous_variant 9/161 NM_153480.2 P2Q8NFR9-1

Frequencies

GnomAD3 genomes
AF:
0.543
AC:
82548
AN:
151888
Hom.:
23255
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.624
Gnomad AMI
AF:
0.609
Gnomad AMR
AF:
0.502
Gnomad ASJ
AF:
0.471
Gnomad EAS
AF:
0.0886
Gnomad SAS
AF:
0.336
Gnomad FIN
AF:
0.591
Gnomad MID
AF:
0.557
Gnomad NFE
AF:
0.549
Gnomad OTH
AF:
0.540
GnomAD3 exomes
AF:
0.480
AC:
120552
AN:
251326
Hom.:
31432
AF XY:
0.478
AC XY:
64874
AN XY:
135846
show subpopulations
Gnomad AFR exome
AF:
0.623
Gnomad AMR exome
AF:
0.443
Gnomad ASJ exome
AF:
0.471
Gnomad EAS exome
AF:
0.0834
Gnomad SAS exome
AF:
0.353
Gnomad FIN exome
AF:
0.593
Gnomad NFE exome
AF:
0.546
Gnomad OTH exome
AF:
0.510
GnomAD4 exome
AF:
0.518
AC:
757817
AN:
1461790
Hom.:
202937
Cov.:
59
AF XY:
0.514
AC XY:
373917
AN XY:
727194
show subpopulations
Gnomad4 AFR exome
AF:
0.623
Gnomad4 AMR exome
AF:
0.449
Gnomad4 ASJ exome
AF:
0.471
Gnomad4 EAS exome
AF:
0.0829
Gnomad4 SAS exome
AF:
0.357
Gnomad4 FIN exome
AF:
0.581
Gnomad4 NFE exome
AF:
0.545
Gnomad4 OTH exome
AF:
0.510
GnomAD4 genome
AF:
0.544
AC:
82648
AN:
152006
Hom.:
23299
Cov.:
32
AF XY:
0.539
AC XY:
40005
AN XY:
74284
show subpopulations
Gnomad4 AFR
AF:
0.625
Gnomad4 AMR
AF:
0.502
Gnomad4 ASJ
AF:
0.471
Gnomad4 EAS
AF:
0.0880
Gnomad4 SAS
AF:
0.337
Gnomad4 FIN
AF:
0.591
Gnomad4 NFE
AF:
0.549
Gnomad4 OTH
AF:
0.545
Alfa
AF:
0.540
Hom.:
52299
Bravo
AF:
0.542
Asia WGS
AF:
0.308
AC:
1067
AN:
3478
EpiCase
AF:
0.542
EpiControl
AF:
0.545

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.011
DANN
Benign
0.36

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.

Other links and lift over

dbSNP: rs279572; hg19: chr3-9952706; COSMIC: COSV55968047; COSMIC: COSV55968047; API