rs3760071

Variant names:

• chr16-57358077-A-G
• rs3760071
• XM_047434449.1:c.-63A>G

Variant summary

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

The XM_047434449.1(CCL22):​c.-63A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,138 control chromosomes in the GnomAD database, including 1,924 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 0.10 (1924 hom., cov: 32)
• Consequence: CCL22 XM_047434449.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL22	XM_047434449.1	c.-63A>G		5_prime_UTR_variant	Exon 1 of 4		XP_047290405.1
CCL22	XM_047434450.1	c.-31+145A>G		intron_variant	Intron 1 of 3		XP_047290406.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15751 AN: 152020 Hom.: 1924 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0543

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.0925

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0182

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0176

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.104 AC: 15768 AN: 152138 Hom.: 1924 Cov.: 32 AF XY: 0.104 AC XY: 7761 AN XY: 74394

African (AFR) AF: 0.290 AC: 12025 AN: 41434

American (AMR) AF: 0.0545 AC: 834 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3470

East Asian (EAS) AF: 0.0921 AC: 477 AN: 5178

South Asian (SAS) AF: 0.163 AC: 787 AN: 4816

European-Finnish (FIN) AF: 0.0182 AC: 193 AN: 10612

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0176 AC: 1195 AN: 68014

Other (OTH) AF: 0.0666 AC: 141 AN: 2116

Alfa AF: 0.0527 Hom.: 306

Bravo AF: 0.109

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.88
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs3760071; hg19: chr16-57391989;