Variant 5-149374486-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_014443.3(IL17B):c.426G>A(p.Pro142Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.011 in 1,612,946 control chromosomes in the GnomAD database, including 134 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0088 ( 8 hom., cov: 33)

Exomes 𝑓: 0.011 ( 126 hom. )

Consequence

IL17B
NM_014443.3 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.59

Variant links:

Genes affected

IL17B (HGNC:5982): (interleukin 17B) The protein encoded by this gene is a T cell-derived cytokine that shares sequence similarity with IL17. This cytokine was reported to stimulate the release of TNF alpha (TNF) and IL1 beta (IL1B) from a monocytic cell line. Immunohistochemical analysis of several nerve tissues indicated that this cytokine is primarily localized to neuronal cell bodies. Alternative splicing results in multiple splice variants. [provided by RefSeq, Dec 2015]

IL17B links:

IL17B (HGNC:):

IL17B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 5-149374486-C-T is Benign according to our data. Variant chr5-149374486-C-T is described in ClinVar as [Benign]. Clinvar id is 789182.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.59 with no splicing effect.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0113 (16453/1460630) while in subpopulation MID AF= 0.0187 (108/5768). AF 95% confidence interval is 0.0159. There are 126 homozygotes in gnomad4_exome. There are 8001 alleles in male gnomad4_exome subpopulation. Median coverage is 30. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL17B	NM_014443.3 linkuse as main transcript	c.426G>A	p.Pro142Pro	synonymous_variant	3/3	ENST00000261796.4	NP_055258.1	Q9UHF5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
IL17B	ENST00000261796.4 linkuse as main transcript	c.426G>A	p.Pro142Pro	synonymous_variant	3/3	1	NM_014443.3	ENSP00000261796.3	Q9UHF5
IL17B	ENST00000505432.1 linkuse as main transcript	n.500G>A		non_coding_transcript_exon_variant	3/3	3
ENSG00000253865	ENST00000521756.1 linkuse as main transcript	n.181-223C>T		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00880

AC:

1339

AN:

152198

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00251

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0107

Gnomad ASJ

AF:

0.0193

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.00198

Gnomad MID

AF:

0.00955

Gnomad NFE

AF:

0.0139

Gnomad OTH

AF:

0.00860

GnomAD3 exomes

AF:

0.00853

AC:

2099

AN:

246150

Hom.:

AF XY:

0.00874

AC XY:

1172

AN XY:

134036

show subpopulations

Gnomad AFR exome

AF:

0.00223

Gnomad AMR exome

AF:

0.00655

Gnomad ASJ exome

AF:

0.0225

Gnomad EAS exome

AF:

0.0000553

Gnomad SAS exome

AF:

0.00216

Gnomad FIN exome

AF:

0.00354

Gnomad NFE exome

AF:

0.0128

Gnomad OTH exome

AF:

0.0109

GnomAD4 exome

AF:

0.0113

AC:

16453

AN:

1460630

Hom.:

126

Cov.:

AF XY:

0.0110

AC XY:

8001

AN XY:

726630

show subpopulations

Gnomad4 AFR exome

AF:

0.00227

Gnomad4 AMR exome

AF:

0.00695

Gnomad4 ASJ exome

AF:

0.0220

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00259

Gnomad4 FIN exome

AF:

0.00360

Gnomad4 NFE exome

AF:

0.0128

Gnomad4 OTH exome

AF:

0.0120

GnomAD4 genome

AF:

0.00878

AC:

1337

AN:

152316

Hom.:

Cov.:

AF XY:

0.00842

AC XY:

627

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.00250

Gnomad4 AMR

AF:

0.0106

Gnomad4 ASJ

AF:

0.0193

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.00198

Gnomad4 NFE

AF:

0.0139

Gnomad4 OTH

AF:

0.00851

Alfa

AF:

0.0116

Hom.:

Bravo

AF:

0.00921

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.0122

EpiControl

AF:

0.0115

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

0.098

DANN

Benign

0.92

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over