rs3017

Variant names:

• chr3-53865553-A-G
• rs3017
• NM_018725.4:c.*245A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018725.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17RB	NM_018725.4	MANE Select	c.*245A>G		3_prime_UTR	Exon 11 of 11	NP_061195.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17RB	ENST00000288167.8	TSL:1 MANE Select	c.*245A>G		3_prime_UTR	Exon 11 of 11	ENSP00000288167.3	Q9NRM6-1
	IL17RB	ENST00000899729.1		c.*245A>G		3_prime_UTR	Exon 13 of 13	ENSP00000569788.1
	IL17RB	ENST00000899731.1		c.*245A>G		3_prime_UTR	Exon 12 of 12	ENSP00000569790.1

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

African (AFR) AF: 0.411 AC: 3982 AN: 9700

American (AMR) AF: 0.300 AC: 3232 AN: 10776

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 3285 AN: 10478

East Asian (EAS) AF: 0.524 AC: 12002 AN: 22906

South Asian (SAS) AF: 0.387 AC: 8945 AN: 23108

European-Finnish (FIN) AF: 0.322 AC: 6094 AN: 18942

Middle Eastern (MID) AF: 0.288 AC: 429 AN: 1488

European-Non Finnish (NFE) AF: 0.338 AC: 65740 AN: 194446

Other (OTH) AF: 0.339 AC: 6482 AN: 19102

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

African (AFR) AF: 0.403 AC: 16748 AN: 41510

American (AMR) AF: 0.330 AC: 5045 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1081 AN: 3468

East Asian (EAS) AF: 0.483 AC: 2496 AN: 5168

South Asian (SAS) AF: 0.379 AC: 1827 AN: 4826

European-Finnish (FIN) AF: 0.313 AC: 3312 AN: 10588

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23258 AN: 67996

Other (OTH) AF: 0.327 AC: 690 AN: 2108

Alfa AF: 0.338 Hom.: 10240

Bravo AF: 0.362

Asia WGS AF: 0.411 AC: 1434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.77
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3017; hg19: chr3-53899580;