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

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

Gnomad4 AFR exome

AF:

0.0859

AC:

2876

AN:

33472

Gnomad4 AMR exome

AF:

0.0930

AC:

4161

AN:

44718

Gnomad4 ASJ exome

AF:

0.0686

AC:

1793

AN:

26134

Gnomad4 EAS exome

AF:

0.144

AC:

5735

AN:

39698

Gnomad4 SAS exome

AF:

0.178

AC:

15338

AN:

86248

Gnomad4 FIN exome

AF:

0.0384

AC:

1974

AN:

51344

Gnomad4 NFE exome

AF:

0.0809

AC:

89974

AN:

1111868

Gnomad4 Remaining exome

AF:

0.0982

AC:

5926

AN:

60366

Heterozygous variant carriers

5784

11567

17351

23134

28918

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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

Gnomad4 AFR

AF:

0.0886

AC:

0.0885597

AN:

0.0885597

Gnomad4 AMR

AF:

0.101

AC:

0.100968

AN:

0.100968

Gnomad4 ASJ

AF:

0.0639

AC:

0.0639401

AN:

0.0639401

Gnomad4 EAS

AF:

0.196

AC:

0.196022

AN:

0.196022

Gnomad4 SAS

AF:

0.185

AC:

0.185347

AN:

0.185347

Gnomad4 FIN

AF:

0.0433

AC:

0.0432692

AN:

0.0432692

Gnomad4 NFE

AF:

0.0787

AC:

0.078692

AN:

0.078692

Gnomad4 OTH

AF:

0.0986

AC:

0.0985782

AN:

0.0985782

Heterozygous variant carriers

637

1274

1912

2549

3186

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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

DANN

Uncertain

0.98

Eigen

Uncertain

0.32

Eigen_PC

Benign

0.026

FATHMM_MKL

Benign

0.20

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)

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over