chr16-57358329-T-C

Variant names:

• chr16-57358329-T-C
• rs223889
• ENST00000941195.1:c.-31+181T>C

Variant summary

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

The ENST00000941195.1(CCL22):​c.-31+181T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 152,070 control chromosomes in the GnomAD database, including 28,951 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 0.59 (28951 hom., cov: 32)
• Consequence: CCL22 ENST00000941195.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 12 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000941195.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL22	ENST00000941195.1		c.-31+181T>C		intron	N/A	ENSP00000611254.1

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89792 AN: 151952 Hom.: 28938 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.591 AC: 89842 AN: 152070 Hom.: 28951 Cov.: 32 AF XY: 0.591 AC XY: 43951 AN XY: 74354

African (AFR) AF: 0.322 AC: 13333 AN: 41464

American (AMR) AF: 0.611 AC: 9345 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2422 AN: 3470

East Asian (EAS) AF: 0.523 AC: 2694 AN: 5154

South Asian (SAS) AF: 0.503 AC: 2420 AN: 4814

European-Finnish (FIN) AF: 0.799 AC: 8471 AN: 10600

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49114 AN: 67964

Other (OTH) AF: 0.633 AC: 1339 AN: 2114

Alfa AF: 0.670 Hom.: 15760

Bravo AF: 0.568

Asia WGS AF: 0.497 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.47
DANN	Benign	0.54
PhyloP100		-1.9
PromoterAI		0.019	Neutral

Splicing

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

Other links and lift over

dbSNP: rs223889; hg19: chr16-57392241;