13-20721055-C-T

Variant names:

• chr13-20721055-C-T
• rs3847993
• NM_001385224.1:c.291-581C>T

Variant summary

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

The NM_001385224.1(IL17D):​c.291-581C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 152,072 control chromosomes in the GnomAD database, including 13,151 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 (13151 hom., cov: 32)
• Consequence: IL17D NM_001385224.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL17D	NM_001385224.1	c.291-581C>T		intron_variant	Intron 1 of 1	ENST00000682841.1	NP_001372153.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL17D	ENST00000682841.1	c.291-581C>T		intron_variant	Intron 1 of 1		NM_001385224.1	ENSP00000508385.1
IL17D	ENST00000304920.3	c.291-581C>T		intron_variant	Intron 2 of 2	1		ENSP00000302924.3
IL17D	ENST00000468605.1	n.*215-581C>T		intron_variant	Intron 2 of 2	3		ENSP00000480610.1

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60706 AN: 151956 Hom.: 13157 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.399 AC: 60716 AN: 152072 Hom.: 13151 Cov.: 32 AF XY: 0.396 AC XY: 29453 AN XY: 74338

African (AFR) AF: 0.267 AC: 11084 AN: 41494

American (AMR) AF: 0.335 AC: 5117 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1693 AN: 3466

East Asian (EAS) AF: 0.236 AC: 1216 AN: 5160

South Asian (SAS) AF: 0.295 AC: 1418 AN: 4810

European-Finnish (FIN) AF: 0.481 AC: 5087 AN: 10566

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.492 AC: 33428 AN: 67980

Other (OTH) AF: 0.443 AC: 936 AN: 2112

Alfa AF: 0.319 Hom.: 885

Bravo AF: 0.385

Asia WGS AF: 0.260 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.34
PhyloP100		-1.5
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: rs3847993; hg19: chr13-21295194;