3-9917263-T-TG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_153460.4(IL17RC):c.-44dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.39 (12370 hom., cov: 0)
  • Exomes 𝑓: 0.34 (36723 hom.)
• Consequence: IL17RC NM_153460.4 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0890

Genes affected

IL17RC (HGNC:18358): (interleukin 17 receptor C) This gene encodes a single-pass type I membrane protein that shares similarity with the interleukin-17 receptor (IL-17RA). Unlike IL-17RA, which is predominantly expressed in hemopoietic cells, and binds with high affinity to only IL-17A, this protein is expressed in nonhemopoietic tissues, and binds both IL-17A and IL-17F with similar affinities. The proinflammatory cytokines, IL-17A and IL-17F, have been implicated in the progression of inflammatory and autoimmune diseases. Multiple alternatively spliced transcript variants encoding different isoforms have been detected for this gene, and it has been proposed that soluble, secreted proteins lacking transmembrane and intracellular domains may function as extracellular antagonists to cytokine signaling. [provided by RefSeq, Feb 2011]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-9917263-T-TG is Benign according to our data. Variant chr3-9917263-T-TG is described in ClinVar as [Benign]. Clinvar id is 2688239.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL17RC	NM_153460.4	c.-44dup		5_prime_UTR_variant	1/19	ENST00000403601.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17RC	ENST00000403601.8	c.-44dup		5_prime_UTR_variant	1/19	1	NM_153460.4	P4

Frequencies

GnomAD3 genomes AF: 0.393 AC: 58895 AN: 149906 Hom.: 12336 Cov.: 0

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.0893

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.338

GnomAD4 exome AF: 0.345 AC: 379929 AN: 1101444 Hom.: 36723 Cov.: 20 AF XY: 0.344 AC XY: 188247 AN XY: 547664

Gnomad4 AFR exome AF: 0.488

Gnomad4 AMR exome AF: 0.307

Gnomad4 ASJ exome AF: 0.299

Gnomad4 EAS exome AF: 0.110

Gnomad4 SAS exome AF: 0.343

Gnomad4 FIN exome AF: 0.380

Gnomad4 NFE exome AF: 0.350

Gnomad4 OTH exome AF: 0.342

GnomAD4 genome AF: 0.393 AC: 58985 AN: 150012 Hom.: 12370 Cov.: 0 AF XY: 0.393 AC XY: 28754 AN XY: 73226

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.0889

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.348

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 32% of patients studied by a panel of primary immunodeficiencies. Number of patients: 30. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs530330109; hg19: chr3-9958947;