Variant 3-57097501-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_017563.5(IL17RD):c.2107+95T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 919,650 control chromosomes in the GnomAD database, including 235,429 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.69 ( 36858 hom., cov: 32)

Exomes 𝑓: 0.71 ( 198571 hom. )

Consequence

IL17RD
NM_017563.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.415

Variant links:

Genes affected

IL17RD (HGNC:17616): (interleukin 17 receptor D) This gene encodes a membrane protein belonging to the interleukin-17 receptor (IL-17R) protein family. The encoded protein is a component of the interleukin-17 receptor signaling complex, and the interaction between this protein and IL-17R does not require the interleukin. The gene product also affects fibroblast growth factor signaling, inhibiting or stimulating growth through MAPK/ERK signaling. Alternate splicing generates multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2016]

IL17RD links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 3-57097501-A-C is Benign according to our data. Variant chr3-57097501-A-C is described in ClinVar as [Benign]. Clinvar id is 1262167.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL17RD	NM_017563.5 linkuse as main transcript	c.2107+95T>G		intron_variant		ENST00000296318.12

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL17RD	ENST00000296318.12 linkuse as main transcript	c.2107+95T>G	intron_variant		1	NM_017563.5	P1	Q8NFM7-1
IL17RD	ENST00000320057.9 linkuse as main transcript	c.1675+95T>G	intron_variant		1			Q8NFM7-2
IL17RD	ENST00000463523.5 linkuse as main transcript	c.1675+95T>G	intron_variant		1			Q8NFM7-2
IL17RD	ENST00000469841.5 linkuse as main transcript	n.2139T>G	non_coding_transcript_exon_variant	12/12	2

Frequencies

GnomAD3 genomes

AF:

0.689

AC:

104738

AN:

151976

Hom.:

36839

Cov.:

show subpopulations

Gnomad AFR

AF:

0.652

Gnomad AMI

AF:

0.711

Gnomad AMR

AF:

0.644

Gnomad ASJ

AF:

0.667

Gnomad EAS

AF:

0.263

Gnomad SAS

AF:

0.718

Gnomad FIN

AF:

0.786

Gnomad MID

AF:

0.722

Gnomad NFE

AF:

0.739

Gnomad OTH

AF:

0.671

GnomAD3 exomes

AF:

0.675

AC:

91525

AN:

135580

Hom.:

32340

AF XY:

0.681

AC XY:

48844

AN XY:

71764

show subpopulations

Gnomad AFR exome

AF:

0.647

Gnomad AMR exome

AF:

0.602

Gnomad ASJ exome

AF:

0.683

Gnomad EAS exome

AF:

0.252

Gnomad SAS exome

AF:

0.754

Gnomad FIN exome

AF:

0.793

Gnomad NFE exome

AF:

0.735

Gnomad OTH exome

AF:

0.694

GnomAD4 exome

AF:

0.712

AC:

546707

AN:

767556

Hom.:

198571

Cov.:

AF XY:

0.714

AC XY:

284359

AN XY:

398224

show subpopulations

Gnomad4 AFR exome

AF:

0.655

Gnomad4 AMR exome

AF:

0.609

Gnomad4 ASJ exome

AF:

0.680

Gnomad4 EAS exome

AF:

0.310

Gnomad4 SAS exome

AF:

0.750

Gnomad4 FIN exome

AF:

0.793

Gnomad4 NFE exome

AF:

0.737

Gnomad4 OTH exome

AF:

0.693

GnomAD4 genome

AF:

0.689

AC:

104805

AN:

152094

Hom.:

36858

Cov.:

AF XY:

0.688

AC XY:

51166

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.652

Gnomad4 AMR

AF:

0.643

Gnomad4 ASJ

AF:

0.667

Gnomad4 EAS

AF:

0.264

Gnomad4 SAS

AF:

0.718

Gnomad4 FIN

AF:

0.786

Gnomad4 NFE

AF:

0.739

Gnomad4 OTH

AF:

0.669

Alfa

AF:

0.706

Hom.:

12525

Bravo

AF:

0.674

Asia WGS

AF:

0.494

AC:

1721

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 09, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.49

DANN

Benign

0.34

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