rs2072069

chr17-34357972-G-A

Variant summary

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

The NM_005408.3(CCL13):c.192-54G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 1,306,394 control chromosomes in the GnomAD database, including 178,665 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 0.47 (17269 hom., cov: 32)
  • Exomes 𝑓: 0.52 (161396 hom.)
• Consequence: CCL13 NM_005408.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279

Genes affected

CCL13 (HGNC:10611): (C-C motif chemokine ligand 13) 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 monocytes, lymphocytes, basophils and eosinophils, but not neutrophils. This chemokine plays a role in accumulation of leukocytes during inflammation. It may also be involved in the recruitment of monocytes into the arterial wall during artherosclerosis. [provided by RefSeq, Sep 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCL13	NM_005408.3	c.192-54G>A		intron_variant		ENST00000225844.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCL13	ENST00000225844.7	c.192-54G>A		intron_variant		1	NM_005408.3	P1
CCL13	ENST00000577681.1	c.85-54G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71210 AN: 151914 Hom.: 17267 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.493

GnomAD4 exome AF: 0.524 AC: 604864 AN: 1154362 Hom.: 161396 AF XY: 0.526 AC XY: 309046 AN XY: 587580

Gnomad4 AFR exome AF: 0.337

Gnomad4 AMR exome AF: 0.317

Gnomad4 ASJ exome AF: 0.616

Gnomad4 EAS exome AF: 0.433

Gnomad4 SAS exome AF: 0.506

Gnomad4 FIN exome AF: 0.483

Gnomad4 NFE exome AF: 0.545

Gnomad4 OTH exome AF: 0.525

GnomAD4 genome AF: 0.469 AC: 71230 AN: 152032 Hom.: 17269 Cov.: 32 AF XY: 0.466 AC XY: 34640 AN XY: 74298

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.494

Alfa AF: 0.505 Hom.: 3398

Bravo AF: 0.458

Asia WGS AF: 0.475 AC: 1652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	9.2
Dann	Benign	0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2072069; hg19: chr17-32684991; COSMIC: COSV56774352; COSMIC: COSV56774352;