16-57364794-C-CTG

Variant names:

• chr16-57364794-C-CTG
• rs57450696
• NM_002990.5:c.*1206_*1207insTG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_002990.5(CCL22):​c.*1206_*1207insTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00042 (1 hom., cov: 19)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CCL22 NM_002990.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948
• Publications: 1 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: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL22	NM_002990.5	c.*1206_*1207insTG		3_prime_UTR_variant	Exon 3 of 3	ENST00000219235.5	NP_002981.2
CCL22	XM_047434449.1	c.*1206_*1207insTG		3_prime_UTR_variant	Exon 4 of 4		XP_047290405.1
CCL22	XM_047434450.1	c.*1206_*1207insTG		3_prime_UTR_variant	Exon 4 of 4		XP_047290406.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL22	ENST00000219235.5	c.*1206_*1207insTG		3_prime_UTR_variant	Exon 3 of 3	1	NM_002990.5	ENSP00000219235.4

Frequencies

GnomAD3 genomes AF: 0.000420 AC: 55 AN: 130864 Hom.: 1 Cov.: 19

Gnomad AFR AF: 0.000574

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000778

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000455

Gnomad SAS AF: 0.000524

Gnomad FIN AF: 0.000264

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000445

Gnomad OTH AF: 0.000550

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 236 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 182

African (AFR) AF: 0.00 AC: 0 AN: 10

American (AMR) AF: 0.00 AC: 0 AN: 8

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 6

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 190

Other (OTH) AF: 0.00 AC: 0 AN: 14

GnomAD4 genome AF: 0.000420 AC: 55 AN: 130894 Hom.: 1 Cov.: 19 AF XY: 0.000399 AC XY: 25 AN XY: 62670

African (AFR) AF: 0.000573 AC: 19 AN: 33180

American (AMR) AF: 0.0000777 AC: 1 AN: 12874

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3300

East Asian (EAS) AF: 0.000457 AC: 2 AN: 4376

South Asian (SAS) AF: 0.000527 AC: 2 AN: 3796

European-Finnish (FIN) AF: 0.000264 AC: 2 AN: 7568

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 238

European-Non Finnish (NFE) AF: 0.000445 AC: 28 AN: 62932

Other (OTH) AF: 0.000543 AC: 1 AN: 1840

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.95
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs57450696; hg19: chr16-57398706;