dbSNP rs3017: IL17RB:c.*245A>G (chr3-53865553-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.133

Publications

21 publications found

Variant links:

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]

IL17RB links:

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]

ACTR8 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17RB	NM_018725.4 link	c.*245A>G		3_prime_UTR_variant	Exon 11 of 11	ENST00000288167.8	NP_061195.2	Q9NRM6-1
ACTR8	XM_005265587.6 link	c.*46-534T>C		intron_variant	Intron 13 of 13		XP_005265644.1	Q9H981-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL17RB	ENST00000288167.8 link	c.*245A>G		3_prime_UTR_variant	Exon 11 of 11	1	NM_018725.4	ENSP00000288167.3		Q9NRM6-1
IL17RB	ENST00000475124.1 link	n.2787A>G		non_coding_transcript_exon_variant	Exon 10 of 10	2

Frequencies

GnomAD3 genomes

AF:

0.361

AC:

54916

AN:

152046

Hom.:

10209

Cov.:

show subpopulations

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.:

AF XY:

0.356

AC XY:

57356

AN XY:

161088

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

3296

6591

9887

13182

16478

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.361

AC:

54952

AN:

152164

Hom.:

10214

Cov.:

AF XY:

0.362

AC XY:

26900

AN XY:

74374

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.342

AC:

23258

AN:

67996

Other (OTH)

AF:

0.327

AC:

690

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1812

3625

5437

7250

9062

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

2.8

(source)

DANN

Benign

0.77

PhyloP100

-0.13

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs3017

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over