rs712043

Variant names:

• chr17-36069307-T-C
• rs712043
• NM_002988.4:c.68-1140T>C

Variant summary

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

The NM_002988.4(CCL18):​c.68-1140T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,164 control chromosomes in the GnomAD database, including 46,854 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 (46854 hom., cov: 32)
• Consequence: CCL18 NM_002988.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL18	NM_002988.4	c.68-1140T>C		intron_variant	Intron 1 of 2	ENST00000616054.2	NP_002979.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL18	ENST00000616054.2	c.68-1140T>C		intron_variant	Intron 1 of 2	1	NM_002988.4	ENSP00000479955.1

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118075 AN: 152046 Hom.: 46788 Cov.: 32

Gnomad AFR AF: 0.944

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.777 AC: 118205 AN: 152164 Hom.: 46854 Cov.: 32 AF XY: 0.778 AC XY: 57887 AN XY: 74394

African (AFR) AF: 0.944 AC: 39189 AN: 41532

American (AMR) AF: 0.760 AC: 11612 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2789 AN: 3472

East Asian (EAS) AF: 0.667 AC: 3444 AN: 5166

South Asian (SAS) AF: 0.776 AC: 3741 AN: 4820

European-Finnish (FIN) AF: 0.734 AC: 7769 AN: 10588

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47168 AN: 67990

Other (OTH) AF: 0.783 AC: 1648 AN: 2106

Alfa AF: 0.729 Hom.: 13371

Bravo AF: 0.786

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.2
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs712043; hg19: chr17-34396667;