chr16-57364795-C-G

Position:

• chr16-57364795-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002990.5(CCL22):​c.*1207C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.75 (32240 hom., cov: 19)
  • Exomes 𝑓: 0.89 (96 hom.)
• Consequence: CCL22 NM_002990.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCL22	NM_002990.5	c.*1207C>G		3_prime_UTR_variant	3/3	ENST00000219235.5
CCL22	XM_047434449.1	c.*1207C>G		3_prime_UTR_variant	4/4
CCL22	XM_047434450.1	c.*1207C>G		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCL22	ENST00000219235.5	c.*1207C>G		3_prime_UTR_variant	3/3	1	NM_002990.5	P1

Frequencies

GnomAD3 genomes AF: 0.753 AC: 92830 AN: 123284 Hom.: 32234 Cov.: 19

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.760

GnomAD4 exome AF: 0.887 AC: 211 AN: 238 Hom.: 96 Cov.: 0 AF XY: 0.886 AC XY: 163 AN XY: 184

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.895

Gnomad4 OTH exome AF: 0.857

GnomAD4 genome AF: 0.753 AC: 92845 AN: 123306 Hom.: 32240 Cov.: 19 AF XY: 0.755 AC XY: 44534 AN XY: 58950

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.862

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.763

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.85
DANN	Benign	0.25

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: rs57186204; hg19: chr16-57398707;