16-57364038-C-T

Variant names:

• chr16-57364038-C-T
• rs170360
• NM_002990.5:c.*450C>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.*450C>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 0.873 in 164,838 control chromosomes in the GnomAD database, including 63,618 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 (58411 hom., cov: 32)
  • Exomes 𝑓: 0.90 (5207 hom.)
• Consequence: CCL22 NM_002990.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 11 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.943 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.*450C>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.*450C>T		3_prime_UTR	Exon 3 of 3	ENSP00000219235.4
	CCL22	ENST00000941195.1		c.*450C>T		3_prime_UTR	Exon 4 of 4	ENSP00000611254.1

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132384 AN: 152066 Hom.: 58399 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.953

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.886

GnomAD4 exome AF: 0.904 AC: 11438 AN: 12654 Hom.: 5207 Cov.: 0 AF XY: 0.904 AC XY: 6058 AN XY: 6704

African (AFR) AF: 0.723 AC: 289 AN: 400

American (AMR) AF: 0.827 AC: 1926 AN: 2330

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 207 AN: 230

East Asian (EAS) AF: 0.857 AC: 559 AN: 652

South Asian (SAS) AF: 0.905 AC: 1223 AN: 1352

European-Finnish (FIN) AF: 0.948 AC: 220 AN: 232

Middle Eastern (MID) AF: 0.882 AC: 30 AN: 34

European-Non Finnish (NFE) AF: 0.944 AC: 6438 AN: 6822

Other (OTH) AF: 0.907 AC: 546 AN: 602

GnomAD4 genome AF: 0.870 AC: 132437 AN: 152184 Hom.: 58411 Cov.: 32 AF XY: 0.869 AC XY: 64634 AN XY: 74404

African (AFR) AF: 0.727 AC: 30143 AN: 41480

American (AMR) AF: 0.824 AC: 12593 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.932 AC: 3235 AN: 3472

East Asian (EAS) AF: 0.878 AC: 4539 AN: 5170

South Asian (SAS) AF: 0.904 AC: 4361 AN: 4824

European-Finnish (FIN) AF: 0.953 AC: 10110 AN: 10612

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.949 AC: 64539 AN: 68022

Other (OTH) AF: 0.888 AC: 1874 AN: 2110

Alfa AF: 0.917 Hom.: 89772

Bravo AF: 0.853

Asia WGS AF: 0.855 AC: 2974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.7
DANN	Benign	0.69
PhyloP100		0.076
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: rs170360; hg19: chr16-57397950;