13-20705895-A-G

Position:

• chr13-20705895-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001385224.1(IL17D):​c.290+1604A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,068 control chromosomes in the GnomAD database, including 33,116 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 0.65 (33116 hom., cov: 31)
• Consequence: IL17D NM_001385224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.965

Genes affected

IL17D (HGNC:5984): (interleukin 17D) The protein encoded by this gene is a cytokine that shares the sequence similarity with IL17. The treatment of endothelial cells with this cytokine has been shown to stimulate the production of other cytokines including IL6, IL8 and CSF2/ GM-CSF. The increased expression of IL8 induced by this cytokine was found to be NF-kappa B-dependent. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL17D	NM_001385224.1	c.290+1604A>G		intron_variant		ENST00000682841.1	NP_001372153.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL17D	ENST00000682841.1	c.290+1604A>G		intron_variant			NM_001385224.1	ENSP00000508385	P1
IL17D	ENST00000304920.3	c.290+1604A>G		intron_variant		1		ENSP00000302924	P1
IL17D	ENST00000468605.1	c.213+1604A>G		intron_variant, NMD_transcript_variant		3		ENSP00000480610

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98184 AN: 151948 Hom.: 33106 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.673

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.646 AC: 98227 AN: 152068 Hom.: 33116 Cov.: 31 AF XY: 0.636 AC XY: 47298 AN XY: 74360

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.665

Alfa AF: 0.722 Hom.: 61873

Bravo AF: 0.625

Asia WGS AF: 0.357 AC: 1243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.30
DANN	Benign	0.24

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: rs735539; hg19: chr13-21280034;