Genetic Variant IL17RB:p.Gln484* (chr3-53865249-C-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_018725.4(IL17RB):c.1450C>T(p.Gln484*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0879 in 1,611,796 control chromosomes in the GnomAD database, including 7,228 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 0.088 ( 710 hom., cov: 32)

Exomes 𝑓: 0.088 ( 6518 hom. )

Consequence

IL17RB
NM_018725.4 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.246

Publications

44 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 -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17RB	NM_018725.4 link	c.1450C>T	p.Gln484*	stop_gained	Exon 11 of 11	ENST00000288167.8	NP_061195.2	Q9NRM6-1
ACTR8	XM_005265587.6 link	c.*46-230G>A		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.1450C>T	p.Gln484*	stop_gained	Exon 11 of 11	1	NM_018725.4	ENSP00000288167.3		Q9NRM6-1
IL17RB	ENST00000475124.1 link	n.2483C>T		non_coding_transcript_exon_variant	Exon 10 of 10	2

Frequencies

GnomAD3 genomes

AF:

0.0880

AC:

13383

AN:

152088

Hom.:

707

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0883

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.0639

Gnomad EAS

AF:

0.196

Gnomad SAS

AF:

0.185

Gnomad FIN

AF:

0.0433

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0787

Gnomad OTH

AF:

0.0948

GnomAD2 exomes

AF:

0.0996

AC:

24849

AN:

249524

AF XY:

0.103

show subpopulations

Gnomad AFR exome

AF:

0.0885

Gnomad AMR exome

AF:

0.0935

Gnomad ASJ exome

AF:

0.0731

Gnomad EAS exome

AF:

0.195

Gnomad FIN exome

AF:

0.0399

Gnomad NFE exome

AF:

0.0791

Gnomad OTH exome

AF:

0.0914

GnomAD4 exome

AF:

0.0879

AC:

128310

AN:

1459590

Hom.:

6518

Cov.:

AF XY:

0.0908

AC XY:

65923

AN XY:

726202

show subpopulations

African (AFR)

AF:

0.0859

AC:

2876

AN:

33472

American (AMR)

AF:

0.0930

AC:

4161

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.0686

AC:

1793

AN:

26134

East Asian (EAS)

AF:

0.144

AC:

5735

AN:

39698

South Asian (SAS)

AF:

0.178

AC:

15338

AN:

86248

European-Finnish (FIN)

AF:

0.0384

AC:

1974

AN:

51344

Middle Eastern (MID)

AF:

0.0928

AC:

533

AN:

5742

European-Non Finnish (NFE)

AF:

0.0809

AC:

89974

AN:

1111868

Other (OTH)

AF:

0.0982

AC:

5926

AN:

60366

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

5784

11567

17351

23134

28918

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3444

6888

10332

13776

17220

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0881

AC:

13413

AN:

152206

Hom.:

710

Cov.:

AF XY:

0.0890

AC XY:

6623

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.0886

AC:

3677

AN:

41520

American (AMR)

AF:

0.101

AC:

1543

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0639

AC:

222

AN:

3472

East Asian (EAS)

AF:

0.196

AC:

1015

AN:

5178

South Asian (SAS)

AF:

0.185

AC:

893

AN:

4818

European-Finnish (FIN)

AF:

0.0433

AC:

459

AN:

10608

Middle Eastern (MID)

AF:

0.0748

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0787

AC:

5352

AN:

68012

Other (OTH)

AF:

0.0986

AC:

208

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

637

1274

1912

2549

3186

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

170

340

510

680

850

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0851

Hom.:

2954

Bravo

AF:

0.0886

TwinsUK

AF:

0.0833

AC:

309

ALSPAC

AF:

0.0760

AC:

293

ESP6500AA

AF:

0.0937

AC:

413

ESP6500EA

AF:

0.0790

AC:

679

ExAC

AF:

0.0986

AC:

11976

Asia WGS

AF:

0.205

AC:

711

AN:

3478

EpiCase

AF:

0.0796

EpiControl

AF:

0.0797

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.055

BayesDel_noAF

Pathogenic

0.29

CADD

Pathogenic

(source)

DANN

Uncertain

0.98

Eigen

Uncertain

0.32

Eigen_PC

Benign

0.026

FATHMM_MKL

Benign

0.20

PhyloP100

0.25

Vest4

0.57

GERP RS

2.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=158/42

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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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