chr13-20723059-T-A

Position:

• chr13-20723059-T-A

Variant summary

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

The NM_001385224.1(IL17D):​c.*1105T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,064 control chromosomes in the GnomAD database, including 12,975 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 0.40 (12974 hom., cov: 33)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: IL17D NM_001385224.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL17D	NM_001385224.1	c.*1105T>A		3_prime_UTR_variant	2/2	ENST00000682841.1	NP_001372153.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL17D	ENST00000682841.1	c.*1105T>A		3_prime_UTR_variant	2/2		NM_001385224.1	ENSP00000508385	P1
IL17D	ENST00000304920.3	c.*1105T>A		3_prime_UTR_variant	3/3	1		ENSP00000302924	P1

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60420 AN: 151946 Hom.: 12982 Cov.: 33

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.444

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.397 AC: 60431 AN: 152062 Hom.: 12974 Cov.: 33 AF XY: 0.394 AC XY: 29291 AN XY: 74322

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.438

Alfa AF: 0.434 Hom.: 1924

Bravo AF: 0.381

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.69
DANN	Benign	0.60

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: rs7787; hg19: chr13-21297198;