chr16-57364905-C-T

Variant names:

• chr16-57364905-C-T
• rs223823
• NM_002990.5:c.*1317C>T

Variant summary

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

The NM_002990.5(CCL22):​c.*1317C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 150,496 control chromosomes in the GnomAD database, including 57,343 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 0.87 (57270 hom., cov: 24)
  • Exomes 𝑓: 0.92 (73 hom.)
• Consequence: CCL22 NM_002990.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737
• Publications: 4 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002990.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL22	NM_002990.5	MANE Select	c.*1317C>T		3_prime_UTR	Exon 3 of 3	NP_002981.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL22	ENST00000219235.5	TSL:1 MANE Select	c.*1317C>T		3_prime_UTR	Exon 3 of 3	ENSP00000219235.4

Frequencies

GnomAD3 genomes AF: 0.867 AC: 130268 AN: 150204 Hom.: 57254 Cov.: 24

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.878

GnomAD4 exome AF: 0.920 AC: 160 AN: 174 Hom.: 73 Cov.: 0 AF XY: 0.921 AC XY: 129 AN XY: 140

African (AFR) AF: 0.750 AC: 3 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AF: 0.750 AC: 3 AN: 4

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.932 AC: 136 AN: 146

Other (OTH) AF: 0.857 AC: 12 AN: 14

GnomAD4 genome AF: 0.867 AC: 130326 AN: 150322 Hom.: 57270 Cov.: 24 AF XY: 0.866 AC XY: 63495 AN XY: 73322

African (AFR) AF: 0.717 AC: 29156 AN: 40676

American (AMR) AF: 0.831 AC: 12544 AN: 15088

Ashkenazi Jewish (ASJ) AF: 0.927 AC: 3218 AN: 3470

East Asian (EAS) AF: 0.888 AC: 4521 AN: 5094

South Asian (SAS) AF: 0.903 AC: 4269 AN: 4728

European-Finnish (FIN) AF: 0.952 AC: 9765 AN: 10254

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.945 AC: 63988 AN: 67724

Other (OTH) AF: 0.880 AC: 1834 AN: 2084

Alfa AF: 0.903 Hom.: 7304

Bravo AF: 0.850

Asia WGS AF: 0.855 AC: 2975 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.77
PhyloP100		-0.74
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs223823; hg19: chr16-57398817;