3-53857070-C-G

Position:

• chr3-53857070-C-G

Variant summary

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

The NM_018725.4(IL17RB):​c.672+84C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 1,425,060 control chromosomes in the GnomAD database, including 88,737 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 0.36 (9877 hom., cov: 32)
  • Exomes 𝑓: 0.35 (78860 hom.)
• Consequence: IL17RB NM_018725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

IL17RB (HGNC:18015): (interleukin 17 receptor B) The protein encoded by this gene is a cytokine receptor. This receptor specifically binds to IL17B and IL17E, but does not bind to IL17 and IL17C. This receptor has been shown to mediate the activation of NF-kappaB and the production of IL8 induced by IL17E. The expression of the rat counterpart of this gene was found to be significantly up-regulated during intestinal inflammation, which suggested the immunoregulatory activity of this receptor. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL17RB	NM_018725.4	c.672+84C>G		intron_variant		ENST00000288167.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17RB	ENST00000288167.8	c.672+84C>G		intron_variant		1	NM_018725.4	P1
IL17RB	ENST00000494338.1	c.624+84C>G		intron_variant		5
IL17RB	ENST00000475124.1	n.677+84C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54046 AN: 151938 Hom.: 9874 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.326

GnomAD4 exome AF: 0.350 AC: 445962 AN: 1273004 Hom.: 78860 AF XY: 0.351 AC XY: 224495 AN XY: 640460

Gnomad4 AFR exome AF: 0.402

Gnomad4 AMR exome AF: 0.291

Gnomad4 ASJ exome AF: 0.317

Gnomad4 EAS exome AF: 0.505

Gnomad4 SAS exome AF: 0.363

Gnomad4 FIN exome AF: 0.311

Gnomad4 NFE exome AF: 0.348

Gnomad4 OTH exome AF: 0.345

GnomAD4 genome AF: 0.356 AC: 54075 AN: 152056 Hom.: 9877 Cov.: 32 AF XY: 0.356 AC XY: 26488 AN XY: 74330

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.322

Alfa AF: 0.219 Hom.: 466

Bravo AF: 0.356

Asia WGS AF: 0.397 AC: 1386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.027
DANN	Benign	0.54

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: rs2276840; hg19: chr3-53891097; COSMIC: COSV55473827; COSMIC: COSV55473827;