rs3214179

Variant names:

• chr16-57358595-AG-A
• rs3214179
• XM_047434449.1:c.10-185delG

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCL22	XM_047434449.1	c.10-185delG		intron_variant	Intron 1 of 3		XP_047290405.1
CCL22	XM_047434450.1	c.-30-185delG		intron_variant	Intron 1 of 3		XP_047290406.1
CCL22	NM_002990.5	c.-221delG		upstream_gene_variant		ENST00000219235.5	NP_002981.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL22	ENST00000219235.5	c.-221delG		upstream_gene_variant		1	NM_002990.5	ENSP00000219235.4

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

African (AFR) AF: 0.172 AC: 7129 AN: 41520

American (AMR) AF: 0.525 AC: 8023 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2057 AN: 3470

East Asian (EAS) AF: 0.522 AC: 2692 AN: 5158

South Asian (SAS) AF: 0.485 AC: 2338 AN: 4816

European-Finnish (FIN) AF: 0.674 AC: 7129 AN: 10572

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.615 AC: 41782 AN: 67958

Other (OTH) AF: 0.535 AC: 1132 AN: 2114

Alfa AF: 0.449 Hom.: 1513

Bravo AF: 0.457

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.3
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs3214179; hg19: chr16-57392507; COSMIC: COSV54659809;