chr13-20705895-A-G

Variant names:

• chr13-20705895-A-G
• rs735539
• NM_001385224.1:c.290+1604A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001385221.1(IL17D):​c.311+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_001385221.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.965
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001385221.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17D	NM_001385224.1	MANE Select	c.290+1604A>G		intron	N/A	NP_001372153.1
	IL17D	NM_001385221.1		c.311+1604A>G		intron	N/A	NP_001372150.1
	IL17D	NM_001385222.1		c.311+1604A>G		intron	N/A	NP_001372151.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL17D	ENST00000682841.1	MANE Select	c.290+1604A>G		intron	N/A	ENSP00000508385.1
	IL17D	ENST00000304920.3	TSL:1	c.290+1604A>G		intron	N/A	ENSP00000302924.3
	IL17D	ENST00000962835.1		c.290+1604A>G		intron	N/A	ENSP00000632894.1

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

African (AFR) AF: 0.572 AC: 23712 AN: 41438

American (AMR) AF: 0.508 AC: 7762 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2508 AN: 3468

East Asian (EAS) AF: 0.221 AC: 1141 AN: 5172

South Asian (SAS) AF: 0.496 AC: 2388 AN: 4814

European-Finnish (FIN) AF: 0.719 AC: 7614 AN: 10588

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.747 AC: 50771 AN: 67992

Other (OTH) AF: 0.665 AC: 1404 AN: 2110

Alfa AF: 0.700 Hom.: 109664

Bravo AF: 0.625

Asia WGS AF: 0.357 AC: 1243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.30
DANN	Benign	0.24
PhyloP100		-0.96
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs735539; hg19: chr13-21280034;