Variant 22-49999855-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001371417.1(IL17REL):c.663C>T(p.Thr221=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00144 in 1,533,916 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0014 ( 2 hom., cov: 33)

Exomes 𝑓: 0.0014 ( 3 hom. )

Consequence

IL17REL
NM_001371417.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.576

Variant links:

Genes affected

IL17REL (HGNC:33808): (interleukin 17 receptor E like) Predicted to enable interleukin-17 receptor activity. Predicted to be involved in cytokine-mediated signaling pathway. [provided by Alliance of Genome Resources, Apr 2022]

IL17REL links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 22-49999855-G-A is Benign according to our data. Variant chr22-49999855-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2653359.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.576 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
IL17REL	NM_001371417.1 linkuse as main transcript	c.663C>T	p.Thr221=	synonymous_variant	7/15	ENST00000695950.1
IL17REL	NM_001371416.1 linkuse as main transcript	c.663C>T	p.Thr221=	synonymous_variant	7/15
IL17REL	NM_001001694.3 linkuse as main transcript	c.447C>T	p.Thr149=	synonymous_variant	7/15
IL17REL	XR_001755245.2 linkuse as main transcript	n.782C>T		non_coding_transcript_exon_variant	7/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
IL17REL	ENST00000695950.1 linkuse as main transcript	c.663C>T	p.Thr221=	synonymous_variant	7/15		NM_001371417.1	A2
IL17REL	ENST00000695951.1 linkuse as main transcript	c.663C>T	p.Thr221=	synonymous_variant	7/15			P2
IL17REL	ENST00000389983.7 linkuse as main transcript	c.*582C>T		3_prime_UTR_variant, NMD_transcript_variant	7/15	2

Frequencies

GnomAD3 genomes

AF:

0.00140

AC:

213

AN:

152166

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000193

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000262

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00782

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00172

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.00146

AC:

192

AN:

131582

Hom.:

AF XY:

0.00146

AC XY:

104

AN XY:

71122

show subpopulations

Gnomad AFR exome

AF:

0.000348

Gnomad AMR exome

AF:

0.000179

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00692

Gnomad NFE exome

AF:

0.00160

Gnomad OTH exome

AF:

0.00110

GnomAD4 exome

AF:

0.00144

AC:

1991

AN:

1381632

Hom.:

Cov.:

AF XY:

0.00141

AC XY:

963

AN XY:

681610

show subpopulations

Gnomad4 AFR exome

AF:

0.000235

Gnomad4 AMR exome

AF:

0.000204

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00638

Gnomad4 NFE exome

AF:

0.00151

Gnomad4 OTH exome

AF:

0.000996

GnomAD4 genome

AF:

0.00140

AC:

213

AN:

152284

Hom.:

Cov.:

AF XY:

0.00165

AC XY:

123

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.000192

Gnomad4 AMR

AF:

0.000261

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00782

Gnomad4 NFE

AF:

0.00172

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.00165

Hom.:

Bravo

AF:

0.000869

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Oct 01, 2023

IL17REL: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

8.4

DANN

Benign

0.91

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