chr16-57358329-T-C

Position:

• chr16-57358329-T-C

Variant summary

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

The XM_047434449.1(CCL22):​c.9+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 XM_047434449.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCL22	XM_047434449.1	c.9+181T>C		intron_variant			XP_047290405.1
CCL22	XM_047434450.1	c.-31+397T>C		intron_variant			XP_047290406.1
		n.57358329T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.723

Gnomad4 OTH AF: 0.633

Alfa AF: 0.677 Hom.: 6073

Bravo AF: 0.568

Asia WGS AF: 0.497 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.47
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs223889; hg19: chr16-57392241;