3-9921132-A-G

Position:

• chr3-9921132-A-G

Variant summary

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

The NM_153460.4(IL17RC):​c.622+163A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 152,062 control chromosomes in the GnomAD database, including 17,787 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 0.47 (17787 hom., cov: 33)
• Consequence: IL17RC NM_153460.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

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]

IL17RC (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL17RC	NM_153460.4	c.622+163A>G		intron_variant		ENST00000403601.8	NP_703190.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL17RC	ENST00000403601.8	c.622+163A>G		intron_variant		1	NM_153460.4	ENSP00000384969.3
ENSG00000288550	ENST00000683484.1	n.577+530A>G		intron_variant				ENSP00000507040.1

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72066 AN: 151944 Hom.: 17780 Cov.: 33

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.474 AC: 72094 AN: 152062 Hom.: 17787 Cov.: 33 AF XY: 0.475 AC XY: 35325 AN XY: 74308

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.506

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.474

Alfa AF: 0.459 Hom.: 27810

Bravo AF: 0.485

Asia WGS AF: 0.678 AC: 2363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.3
DANN	Benign	0.52

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: rs376511; hg19: chr3-9962816;