3-9911022-A-G

Variant names:

• chr3-9911022-A-G
• rs279572
• NM_153480.2:c.960A>G

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_153480.2(IL17RE):​c.960A>G​(p.Thr320Thr) 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
• Publications: 19 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153480.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17RE	NM_153480.2	MANE Select	c.960A>G	p.Thr320Thr	synonymous	Exon 9 of 16	NP_705613.1
	IL17RE	NM_153483.2		c.1080A>G	p.Thr360Thr	synonymous	Exon 10 of 17	NP_705616.2
	IL17RE	NM_153481.2		c.612A>G	p.Thr204Thr	synonymous	Exon 7 of 14	NP_705614.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17RE	ENST00000383814.8	TSL:1 MANE Select	c.960A>G	p.Thr320Thr	synonymous	Exon 9 of 16	ENSP00000373325.3
	IL17RE	ENST00000421412.5	TSL:1	c.1059A>G	p.Thr353Thr	synonymous	Exon 10 of 17	ENSP00000404916.1
	IL17RE	ENST00000454190.6	TSL:2	c.960A>G	p.Thr320Thr	synonymous	Exon 9 of 16	ENSP00000388086.2

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

GnomAD2 exomes AF: 0.480 AC: 120552 AN: 251326 AF XY: 0.478

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 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

African (AFR) AF: 0.623 AC: 20853 AN: 33480

American (AMR) AF: 0.449 AC: 20080 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 12309 AN: 26136

East Asian (EAS) AF: 0.0829 AC: 3292 AN: 39700

South Asian (SAS) AF: 0.357 AC: 30771 AN: 86256

European-Finnish (FIN) AF: 0.581 AC: 31050 AN: 53412

Middle Eastern (MID) AF: 0.545 AC: 3141 AN: 5768

European-Non Finnish (NFE) AF: 0.545 AC: 605545 AN: 1111926

Other (OTH) AF: 0.510 AC: 30776 AN: 60390

GnomAD4 genome AF: 0.544 AC: 82648 AN: 152006 Hom.: 23299 Cov.: 32 AF XY: 0.539 AC XY: 40005 AN XY: 74284

African (AFR) AF: 0.625 AC: 25883 AN: 41442

American (AMR) AF: 0.502 AC: 7668 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1636 AN: 3470

East Asian (EAS) AF: 0.0880 AC: 454 AN: 5158

South Asian (SAS) AF: 0.337 AC: 1629 AN: 4828

European-Finnish (FIN) AF: 0.591 AC: 6232 AN: 10548

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37282 AN: 67964

Other (OTH) AF: 0.545 AC: 1150 AN: 2112

Alfa AF: 0.542 Hom.: 79006

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.011
DANN	Benign	0.36
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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