rs4687753

Positions:

• chr3-53861434-A-C

Variant summary

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

The ENST00000288167.8(IL17RB):​c.946+1206A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,024 control chromosomes in the GnomAD database, including 10,122 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 (10122 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: IL17RB ENST00000288167.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.497

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL17RB	NM_018725.4	c.946+1206A>C		intron_variant		ENST00000288167.8	NP_061195.2
ACTR8	XM_005265587.6	c.*3631T>G		3_prime_UTR_variant	14/14		XP_005265644.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL17RB	ENST00000288167.8	c.946+1206A>C		intron_variant		1	NM_018725.4	ENSP00000288167	P1
	ENST00000607783.1	n.143T>G		non_coding_transcript_exon_variant	1/1
IL17RB	ENST00000494338.1	c.898+1206A>C		intron_variant		5		ENSP00000418638
IL17RB	ENST00000475124.1	n.1979+1206A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54675 AN: 151906 Hom.: 10117 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.332

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.360 AC: 54711 AN: 152024 Hom.: 10122 Cov.: 32 AF XY: 0.360 AC XY: 26753 AN XY: 74306

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.328

Alfa AF: 0.348 Hom.: 1142

Bravo AF: 0.361

Asia WGS AF: 0.398 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.39

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: rs4687753; hg19: chr3-53895461;