rs73557194

Variant names:

• chr16-57361878-A-G
• rs73557194
• NM_002990.5:c.197+1318A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-57361878-A-G
• chr16-57361878-A-T

Variant summary

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

The NM_002990.5(CCL22):​c.197+1318A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0378 in 152,276 control chromosomes in the GnomAD database, including 229 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 0.038 (229 hom., cov: 32)
• Consequence: CCL22 NM_002990.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.42
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL22	NM_002990.5	c.197+1318A>G		intron_variant	Intron 2 of 2	ENST00000219235.5	NP_002981.2
CCL22	XM_047434449.1	c.236+1318A>G		intron_variant	Intron 3 of 3		XP_047290405.1
CCL22	XM_047434450.1	c.197+1318A>G		intron_variant	Intron 3 of 3		XP_047290406.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL22	ENST00000219235.5	c.197+1318A>G		intron_variant	Intron 2 of 2	1	NM_002990.5	ENSP00000219235.4

Frequencies

GnomAD3 genomes AF: 0.0378 AC: 5750 AN: 152158 Hom.: 231 Cov.: 32

Gnomad AFR AF: 0.0524

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0541

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.0345

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.0449

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

GnomAD4 genome AF: 0.0378 AC: 5749 AN: 152276 Hom.: 229 Cov.: 32 AF XY: 0.0390 AC XY: 2906 AN XY: 74454

African (AFR) AF: 0.0525 AC: 2183 AN: 41542

American (AMR) AF: 0.0539 AC: 824 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00778 AC: 27 AN: 3470

East Asian (EAS) AF: 0.228 AC: 1178 AN: 5172

South Asian (SAS) AF: 0.0219 AC: 106 AN: 4830

European-Finnish (FIN) AF: 0.0345 AC: 366 AN: 10612

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0140 AC: 952 AN: 68034

Other (OTH) AF: 0.0440 AC: 93 AN: 2116

Alfa AF: 0.0306 Hom.: 485

Bravo AF: 0.0432

Asia WGS AF: 0.100 AC: 350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.6
DANN	Benign	0.63
PhyloP100		2.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs73557194; hg19: chr16-57395790;