rs3214179

Positions:

• chr16-57358595-AG-A
• chr16-57358595-AG-AGG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The XM_047434449.1(CCL22):​c.10-185delG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.48 (20368 hom., cov: 0)
• Consequence: CCL22 XM_047434449.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29

Genes affected

CCL22 (HGNC:10621): (C-C motif chemokine ligand 22) This antimicrobial gene is one of several Cys-Cys (CC) cytokine genes clustered on the q arm of chromosome 16. 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, dendritic cells, natural killer cells and for chronically activated T lymphocytes. It also displays a mild activity for primary activated T lymphocytes and has no chemoattractant activity for neutrophils, eosinophils and resting T lymphocytes. The product of this gene binds to chemokine receptor CCR4. This chemokine may play a role in the trafficking of activated T lymphocytes to inflammatory sites and other aspects of activated T lymphocyte physiology. [provided by RefSeq, Sep 2014]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCL22	XM_047434449.1	c.10-185delG		intron_variant			XP_047290405.1
CCL22	XM_047434450.1	c.-30-185delG		intron_variant			XP_047290406.1
		n.57358596delG		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72823 AN: 151978 Hom.: 20351 Cov.: 0

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.479 AC: 72852 AN: 152096 Hom.: 20368 Cov.: 0 AF XY: 0.482 AC XY: 35816 AN XY: 74336

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.535

Alfa AF: 0.449 Hom.: 1513

Bravo AF: 0.457

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3214179; hg19: chr16-57392507;