Genetic Variant IL17RB:c.672+84C>G (chr3-53857070-C-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.672+84C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 1,425,060 control chromosomes in the GnomAD database, including 88,737 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.36 ( 9877 hom., cov: 32)

Exomes 𝑓: 0.35 ( 78860 hom. )

Consequence

IL17RB
NM_018725.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

Publications

11 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:

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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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 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.672+84C>G		intron	N/A	NP_061195.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IL17RB	ENST00000288167.8	TSL:1 MANE Select	c.672+84C>G	intron	N/A	ENSP00000288167.3	Q9NRM6-1
IL17RB	ENST00000899729.1		c.846+84C>G	intron	N/A	ENSP00000569788.1
IL17RB	ENST00000899731.1		c.846+84C>G	intron	N/A	ENSP00000569790.1

Frequencies

GnomAD3 genomes

AF:

0.356

AC:

54046

AN:

151938

Hom.:

9874

Cov.:

show subpopulations

Gnomad AFR

AF:

0.390

Gnomad AMI

AF:

0.450

Gnomad AMR

AF:

0.329

Gnomad ASJ

AF:

0.311

Gnomad EAS

AF:

0.481

Gnomad SAS

AF:

0.352

Gnomad FIN

AF:

0.313

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.341

Gnomad OTH

AF:

0.326

GnomAD4 exome

AF:

0.350

AC:

445962

AN:

1273004

Hom.:

78860

AF XY:

0.351

AC XY:

224495

AN XY:

640460

show subpopulations

African (AFR)

AF:

0.402

AC:

11849

AN:

29506

American (AMR)

AF:

0.291

AC:

12584

AN:

43250

Ashkenazi Jewish (ASJ)

AF:

0.317

AC:

7591

AN:

23924

East Asian (EAS)

AF:

0.505

AC:

19611

AN:

38806

South Asian (SAS)

AF:

0.363

AC:

28769

AN:

79294

European-Finnish (FIN)

AF:

0.311

AC:

16281

AN:

52274

Middle Eastern (MID)

AF:

0.284

AC:

1083

AN:

3808

European-Non Finnish (NFE)

AF:

0.348

AC:

329581

AN:

948160

Other (OTH)

AF:

0.345

AC:

18613

AN:

53982

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

14552

29103

43655

58206

72758

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10248

20496

30744

40992

51240

<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:

0.356

AC:

54075

AN:

152056

Hom.:

9877

Cov.:

AF XY:

0.356

AC XY:

26488

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.389

AC:

16154

AN:

41478

American (AMR)

AF:

0.329

AC:

5025

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.311

AC:

1080

AN:

3470

East Asian (EAS)

AF:

0.481

AC:

2484

AN:

5168

South Asian (SAS)

AF:

0.352

AC:

1696

AN:

4820

European-Finnish (FIN)

AF:

0.313

AC:

3309

AN:

10566

Middle Eastern (MID)

AF:

0.289

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.341

AC:

23153

AN:

67960

Other (OTH)

AF:

0.322

AC:

680

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1778

3557

5335

7114

8892

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

530

1060

1590

2120

2650

<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:

0.219

Hom.:

466

Bravo

AF:

0.356

Asia WGS

AF:

0.397

AC:

1386

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.027

(source)

DANN

Benign

0.54

PhyloP100

-1.4

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over