chr3-9906313-C-T

Position:

• chr3-9906313-C-T

Variant summary

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

The NM_153480.2(IL17RE):​c.269-51C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 1,002,022 control chromosomes in the GnomAD database, including 139,617 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 0.56 (24363 hom., cov: 32)
  • Exomes 𝑓: 0.51 (115254 hom.)
• Consequence: IL17RE NM_153480.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL17RE	NM_153480.2	c.269-51C>T		intron_variant		ENST00000383814.8	NP_705613.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL17RE	ENST00000383814.8	c.269-51C>T		intron_variant		1	NM_153480.2	ENSP00000373325.3

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84354 AN: 151872 Hom.: 24316 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.0839

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.550

GnomAD3 exomes AF: 0.490 AC: 112813 AN: 230278 Hom.: 29711 AF XY: 0.489 AC XY: 60874 AN XY: 124522

Gnomad AFR exome AF: 0.668

Gnomad AMR exome AF: 0.457

Gnomad ASJ exome AF: 0.467

Gnomad EAS exome AF: 0.0808

Gnomad SAS exome AF: 0.417

Gnomad FIN exome AF: 0.587

Gnomad NFE exome AF: 0.545

Gnomad OTH exome AF: 0.514

GnomAD4 exome AF: 0.508 AC: 431909 AN: 850032 Hom.: 115254 Cov.: 11 AF XY: 0.506 AC XY: 224339 AN XY: 443442

Gnomad4 AFR exome AF: 0.661

Gnomad4 AMR exome AF: 0.464

Gnomad4 ASJ exome AF: 0.464

Gnomad4 EAS exome AF: 0.0815

Gnomad4 SAS exome AF: 0.418

Gnomad4 FIN exome AF: 0.579

Gnomad4 NFE exome AF: 0.538

Gnomad4 OTH exome AF: 0.515

GnomAD4 genome AF: 0.556 AC: 84458 AN: 151990 Hom.: 24363 Cov.: 32 AF XY: 0.552 AC XY: 41000 AN XY: 74298

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.0833

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.556

Alfa AF: 0.537 Hom.: 11171

Bravo AF: 0.555

Asia WGS AF: 0.333 AC: 1155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.41
DANN	Benign	0.68
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs279581; hg19: chr3-9947997;