rs170359

chr16-57361752-G-Achr16-57361752-G-Cchr16-57361752-G-T

Variant summary

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

The NM_002990.5(CCL22):c.197+1192G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 151,996 control chromosomes in the GnomAD database, including 51,083 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 0.79 (51083 hom., cov: 30)
• Consequence: CCL22 NM_002990.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.781

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCL22	NM_002990.5	c.197+1192G>A		intron_variant		ENST00000219235.5
CCL22	XM_047434449.1	c.236+1192G>A		intron_variant
CCL22	XM_047434450.1	c.197+1192G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCL22	ENST00000219235.5	c.197+1192G>A		intron_variant		1	NM_002990.5	P1

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120153 AN: 151878 Hom.: 51071 Cov.: 30

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.953

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.791 AC: 120206 AN: 151996 Hom.: 51083 Cov.: 30 AF XY: 0.793 AC XY: 58927 AN XY: 74300

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.953

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.842

Alfa AF: 0.919 Hom.: 82987

Bravo AF: 0.762

Asia WGS AF: 0.843 AC: 2932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.40
Dann	Benign	0.68

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: rs170359; hg19: chr16-57395664;