16-57359718-C-T

Position:

• chr16-57359718-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.74-719C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 151,100 control chromosomes in the GnomAD database, including 41,356 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 0.71 (41356 hom., cov: 30)
• Consequence: CCL22 NM_002990.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCL22	NM_002990.5	c.74-719C>T		intron_variant		ENST00000219235.5
CCL22	XM_047434449.1	c.113-719C>T		intron_variant
CCL22	XM_047434450.1	c.74-719C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCL22	ENST00000219235.5	c.74-719C>T		intron_variant		1	NM_002990.5	P1

Frequencies

GnomAD3 genomes AF: 0.713 AC: 107622 AN: 150982 Hom.: 41342 Cov.: 30

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.761

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.762

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.713 AC: 107677 AN: 151100 Hom.: 41356 Cov.: 30 AF XY: 0.709 AC XY: 52344 AN XY: 73780

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.766

Alfa AF: 0.755 Hom.: 3037

Bravo AF: 0.688

Asia WGS AF: 0.589 AC: 2048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.11
DANN	Benign	0.56

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: rs223817; hg19: chr16-57393630;