17-36070248-C-T

Position:

• chr17-36070248-C-T

Variant summary

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

The NM_002988.4(CCL18):​c.68-199C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 540,750 control chromosomes in the GnomAD database, including 147,415 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 0.78 (46675 hom., cov: 31)
  • Exomes 𝑓: 0.72 (100740 hom.)
• Consequence: CCL18 NM_002988.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

CCL18 (HGNC:10616): (C-C motif chemokine ligand 18) This antimicrobial gene is one of several Cys-Cys (CC) cytokine genes clustered on the q arm of chromosome 17. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The CC cytokines are proteins characterized by two adjacent cysteines. The cytokine encoded by this gene displays chemotactic activity for naive T cells, CD4+ and CD8+ T cells and nonactivated lymphocytes, but not for monocytes or granulocytes. This chemokine attracts naive T lymphocytes toward dendritic cells and activated macrophages in lymph nodes. It may play a role in both humoral and cell-mediated immunity responses. [provided by RefSeq, Sep 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCL18	NM_002988.4	c.68-199C>T		intron_variant		ENST00000616054.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCL18	ENST00000616054.2	c.68-199C>T		intron_variant		1	NM_002988.4	P1

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117897 AN: 152062 Hom.: 46611 Cov.: 31

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.776

GnomAD4 exome AF: 0.717 AC: 278723 AN: 388568 Hom.: 100740 AF XY: 0.721 AC XY: 146315 AN XY: 203014

Gnomad4 AFR exome AF: 0.939

Gnomad4 AMR exome AF: 0.760

Gnomad4 ASJ exome AF: 0.788

Gnomad4 EAS exome AF: 0.665

Gnomad4 SAS exome AF: 0.783

Gnomad4 FIN exome AF: 0.718

Gnomad4 NFE exome AF: 0.695

Gnomad4 OTH exome AF: 0.742

GnomAD4 genome AF: 0.776 AC: 118024 AN: 152182 Hom.: 46675 Cov.: 31 AF XY: 0.777 AC XY: 57778 AN XY: 74372

Gnomad4 AFR AF: 0.939

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.803

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.780

Alfa AF: 0.732 Hom.: 4896

Bravo AF: 0.784

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs854472; hg19: chr17-34397608;