rs172155

Positions:

• chr3-9908954-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153480.2(IL17RE):​c.736-263G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,782 control chromosomes in the GnomAD database, including 22,461 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 (22461 hom., cov: 30)
• Consequence: IL17RE NM_153480.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.905

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL17RE	NM_153480.2	c.736-263G>A		intron_variant		ENST00000383814.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17RE	ENST00000383814.8	c.736-263G>A		intron_variant		1	NM_153480.2	P2

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81183 AN: 151666 Hom.: 22426 Cov.: 30

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.0887

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.532

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.535 AC: 81269 AN: 151782 Hom.: 22461 Cov.: 30 AF XY: 0.531 AC XY: 39344 AN XY: 74160

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.0881

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.536

Alfa AF: 0.536 Hom.: 10149

Bravo AF: 0.533

Asia WGS AF: 0.306 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.38

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: rs172155; hg19: chr3-9950638;