3-53858614-T-G

Variant summary

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

The NM_018725.4(IL17RB):c.748-105T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 1,503,852 control chromosomes in the GnomAD database, including 186,641 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 (23313 hom., cov: 32)
  • Exomes 𝑓: 0.48 (163328 hom.)
• Consequence: IL17RB NM_018725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.64

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 = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL17RB	NM_018725.4	c.748-105T>G		intron_variant		ENST00000288167.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17RB	ENST00000288167.8	c.748-105T>G		intron_variant		1	NM_018725.4	P1
IL17RB	ENST00000494338.1	c.700-105T>G		intron_variant		5
IL17RB	ENST00000475124.1	n.1676T>G		non_coding_transcript_exon_variant	8/10	2

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81852 AN: 151942 Hom.: 23268 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.519

GnomAD4 exome AF: 0.479 AC: 647899 AN: 1351792 Hom.: 163328 Cov.: 33 AF XY: 0.484 AC XY: 320103 AN XY: 661892

Gnomad4 AFR exome AF: 0.649

Gnomad4 AMR exome AF: 0.677

Gnomad4 ASJ exome AF: 0.441

Gnomad4 EAS exome AF: 0.948

Gnomad4 SAS exome AF: 0.657

Gnomad4 FIN exome AF: 0.413

Gnomad4 NFE exome AF: 0.442

Gnomad4 OTH exome AF: 0.506

GnomAD4 genome AF: 0.539 AC: 81949 AN: 152060 Hom.: 23313 Cov.: 32 AF XY: 0.545 AC XY: 40479 AN XY: 74286

Gnomad4 AFR AF: 0.645

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.949

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.520

Alfa AF: 0.424 Hom.: 2252

Bravo AF: 0.556

Asia WGS AF: 0.803 AC: 2791 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	9.3
Dann	Benign	0.55

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: rs9840079; hg19: chr3-53892641;