3-57097501-A-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.415

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]

ACMG classification

Verdict is Benign. Variant got -14 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_single_submitter, 1 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	c.2107+95T>G		intron_variant		ENST00000296318.12

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104738 AN: 151976 Hom.: 36839 Cov.: 32

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

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.: 10 AF XY: 0.714 AC XY: 284359 AN XY: 398224

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.: 32 AF XY: 0.688 AC XY: 51166 AN XY: 74352

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:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 09, 2018

- -

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

Other links and lift over

dbSNP: rs6764188; hg19: chr3-57131529; COSMIC: COSV56339083;