chr3-53865553-A-G

Position:

• chr3-53865553-A-G

Variant summary

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

The NM_018725.4(IL17RB):​c.*245A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 463,110 control chromosomes in the GnomAD database, including 30,347 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 (10214 hom., cov: 33)
  • Exomes 𝑓: 0.35 (20133 hom.)
• Consequence: IL17RB NM_018725.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

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]

ACTR8 (HGNC:14672): (actin related protein 8) Predicted to enable ATP binding activity. Predicted to be involved in chromatin remodeling; double-strand break repair; and regulation of transcription, DNA-templated. Located in centrosome and nucleoplasm. Part of Ino80 complex. [provided by Alliance of Genome Resources, Apr 2022]

IL17RB (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• 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.*245A>G		3_prime_UTR_variant	11/11	ENST00000288167.8	NP_061195.2
ACTR8	XM_005265587.6	c.*46-534T>C		intron_variant			XP_005265644.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL17RB	ENST00000288167.8	c.*245A>G		3_prime_UTR_variant	11/11	1	NM_018725.4	ENSP00000288167.3
IL17RB	ENST00000475124.1	n.2787A>G		non_coding_transcript_exon_variant	10/10	2

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54916 AN: 152046 Hom.: 10209 Cov.: 33

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.331

GnomAD4 exome AF: 0.354 AC: 110191 AN: 310946 Hom.: 20133 Cov.: 3 AF XY: 0.356 AC XY: 57356 AN XY: 161088

Gnomad4 AFR exome AF: 0.411

Gnomad4 AMR exome AF: 0.300

Gnomad4 ASJ exome AF: 0.314

Gnomad4 EAS exome AF: 0.524

Gnomad4 SAS exome AF: 0.387

Gnomad4 FIN exome AF: 0.322

Gnomad4 NFE exome AF: 0.338

Gnomad4 OTH exome AF: 0.339

GnomAD4 genome AF: 0.361 AC: 54952 AN: 152164 Hom.: 10214 Cov.: 33 AF XY: 0.362 AC XY: 26900 AN XY: 74374

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.327

Alfa AF: 0.336 Hom.: 8458

Bravo AF: 0.362

Asia WGS AF: 0.411 AC: 1434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.77

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: rs3017; hg19: chr3-53899580;