chr16-57364038-C-T

Position:

• chr16-57364038-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCL22	NM_002990.5	c.*450C>T		3_prime_UTR_variant	3/3	ENST00000219235.5	NP_002981.2
CCL22	XM_047434449.1	c.*450C>T		3_prime_UTR_variant	4/4		XP_047290405.1
CCL22	XM_047434450.1	c.*450C>T		3_prime_UTR_variant	4/4		XP_047290406.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCL22	ENST00000219235.5	c.*450C>T		3_prime_UTR_variant	3/3	1	NM_002990.5	ENSP00000219235.4

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

Gnomad4 AFR exome AF: 0.723

Gnomad4 AMR exome AF: 0.827

Gnomad4 ASJ exome AF: 0.900

Gnomad4 EAS exome AF: 0.857

Gnomad4 SAS exome AF: 0.905

Gnomad4 FIN exome AF: 0.948

Gnomad4 NFE exome AF: 0.944

Gnomad4 OTH exome AF: 0.907

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

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.932

Gnomad4 EAS AF: 0.878

Gnomad4 SAS AF: 0.904

Gnomad4 FIN AF: 0.953

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.888

Alfa AF: 0.926 Hom.: 64107

Bravo AF: 0.853

Asia WGS AF: 0.855 AC: 2974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.7
DANN	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs170360; hg19: chr16-57397950;