rs279572

Positions:

• chr3-9911022-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_153480.2(IL17RE):​c.960A>G​(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: 𝑓 0.54 (23299 hom., cov: 32)
  • Exomes 𝑓: 0.52 (202937 hom.)
• Consequence: IL17RE NM_153480.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

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]

ACMG classification

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
IL17RE	NM_153480.2	c.960A>G	p.Thr320=	synonymous_variant	9/16	ENST00000383814.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17RE	ENST00000383814.8	c.960A>G	p.Thr320=	synonymous_variant	9/16	1	NM_153480.2	P2

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82548 AN: 151888 Hom.: 23255 Cov.: 32

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

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

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

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

Other links and lift over

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