chr3-9908954-G-A

Variant names:

• chr3-9908954-G-A
• rs172155
• NM_153480.2:c.736-263G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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 -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 rank	MANE	Protein	UniProt
IL17RE	NM_153480.2	c.736-263G>A		intron_variant	Intron 7 of 15	ENST00000383814.8	NP_705613.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL17RE	ENST00000383814.8	c.736-263G>A		intron_variant	Intron 7 of 15	1	NM_153480.2	ENSP00000373325.3

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

African (AFR) AF: 0.597 AC: 24676 AN: 41334

American (AMR) AF: 0.501 AC: 7633 AN: 15250

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

East Asian (EAS) AF: 0.0881 AC: 455 AN: 5164

South Asian (SAS) AF: 0.338 AC: 1620 AN: 4800

European-Finnish (FIN) AF: 0.590 AC: 6216 AN: 10538

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37180 AN: 67910

Other (OTH) AF: 0.536 AC: 1132 AN: 2112

Alfa AF: 0.536 Hom.: 11386

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
PhyloP100		0.91
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: rs172155; hg19: chr3-9950638;