5-43360163-C-G

Variant names:

• chr5-43360163-C-G
• rs11950448
• XR_427660.3:n.519-2491G>C

Variant summary

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

The XR_427660.3(CCL28):​n.519-2491G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,910 control chromosomes in the GnomAD database, including 17,484 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 (17484 hom., cov: 31)
• Consequence: CCL28 XR_427660.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348

Genes affected

CCL28 (HGNC:17700): (C-C motif chemokine ligand 28) This antimicrobial gene belongs to the subfamily of small cytokine CC genes. 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 resting CD4 or CD8 T cells and eosinophils. The product of this gene binds to chemokine receptors CCR3 and CCR10. This chemokine may play a role in the physiology of extracutaneous epithelial tissues, including diverse mucosal organs. Multiple transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Sep 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL28	XR_427660.3	n.519-2491G>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71814 AN: 151792 Hom.: 17497 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.473 AC: 71821 AN: 151910 Hom.: 17484 Cov.: 31 AF XY: 0.470 AC XY: 34909 AN XY: 74202

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.494

Alfa AF: 0.361 Hom.: 969

Bravo AF: 0.467

Asia WGS AF: 0.255 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11950448; hg19: chr5-43360265;