dbSNP rs2276840: 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17RB	NM_018725.4 link	c.672+84C>G		intron_variant	Intron 7 of 10	ENST00000288167.8	NP_061195.2	Q9NRM6-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
IL17RB	ENST00000288167.8 link	c.672+84C>G	intron_variant	Intron 7 of 10	1	NM_018725.4	ENSP00000288167.3	Q9NRM6-1
IL17RB	ENST00000494338.1 link	c.624+84C>G	intron_variant	Intron 6 of 9	5		ENSP00000418638.1	C9IZN0
IL17RB	ENST00000475124.1 link	n.677+84C>G	intron_variant	Intron 7 of 9	2

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over