Genetic Variant IL17RB:c.748-105T>G (chr3-53858614-T-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.748-105T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 1,503,852 control chromosomes in the GnomAD database, including 186,641 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 0.54 ( 23313 hom., cov: 32)

Exomes 𝑓: 0.48 ( 163328 hom. )

Consequence

IL17RB
NM_018725.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.64

Publications

17 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 = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17RB	NM_018725.4 link	c.748-105T>G		intron_variant	Intron 8 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.748-105T>G	intron_variant	Intron 8 of 10	1	NM_018725.4	ENSP00000288167.3	Q9NRM6-1
IL17RB	ENST00000475124.1 link	n.1676T>G	non_coding_transcript_exon_variant	Exon 8 of 10	2
IL17RB	ENST00000494338.1 link	c.700-105T>G	intron_variant	Intron 7 of 9	5		ENSP00000418638.1	C9IZN0

Frequencies

GnomAD3 genomes

AF:

0.539

AC:

81852

AN:

151942

Hom.:

23268

Cov.:

show subpopulations

Gnomad AFR

AF:

0.645

Gnomad AMI

AF:

0.565

Gnomad AMR

AF:

0.605

Gnomad ASJ

AF:

0.435

Gnomad EAS

AF:

0.949

Gnomad SAS

AF:

0.666

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.443

Gnomad OTH

AF:

0.519

GnomAD4 exome

AF:

0.479

AC:

647899

AN:

1351792

Hom.:

163328

Cov.:

AF XY:

0.484

AC XY:

320103

AN XY:

661892

show subpopulations

African (AFR)

AF:

0.649

AC:

19860

AN:

30598

American (AMR)

AF:

0.677

AC:

22121

AN:

32670

Ashkenazi Jewish (ASJ)

AF:

0.441

AC:

9938

AN:

22560

East Asian (EAS)

AF:

0.948

AC:

33615

AN:

35476

South Asian (SAS)

AF:

0.657

AC:

47321

AN:

71972

European-Finnish (FIN)

AF:

0.413

AC:

16672

AN:

40410

Middle Eastern (MID)

AF:

0.469

AC:

2565

AN:

5468

European-Non Finnish (NFE)

AF:

0.442

AC:

467320

AN:

1056362

Other (OTH)

AF:

0.506

AC:

28487

AN:

56276

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

15443

30885

46328

61770

77213

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14892

29784

44676

59568

74460

<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:

0.539

AC:

81949

AN:

152060

Hom.:

23313

Cov.:

AF XY:

0.545

AC XY:

40479

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.645

AC:

26771

AN:

41482

American (AMR)

AF:

0.606

AC:

9258

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.435

AC:

1509

AN:

3470

East Asian (EAS)

AF:

0.949

AC:

4910

AN:

5174

South Asian (SAS)

AF:

0.667

AC:

3208

AN:

4812

European-Finnish (FIN)

AF:

0.421

AC:

4452

AN:

10568

Middle Eastern (MID)

AF:

0.517

AC:

152

AN:

294

European-Non Finnish (NFE)

AF:

0.443

AC:

30079

AN:

67960

Other (OTH)

AF:

0.520

AC:

1096

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1851

3702

5552

7403

9254

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

712

1424

2136

2848

3560

<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:

0.431

Hom.:

2414

Bravo

AF:

0.556

Asia WGS

AF:

0.803

AC:

2791

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

9.3

(source)

DANN

Benign

0.55

PhyloP100

2.6

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