chr16-57411464-T-C

Variant names:

• chr16-57411464-T-C
• rs223900
• NM_002987.3:c.-59-2410T>C

Variant summary

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

The NM_002987.3(CCL17):​c.-59-2410T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,226 control chromosomes in the GnomAD database, including 45,664 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 0.77 (45664 hom., cov: 33)
• Consequence: CCL17 NM_002987.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655
• Publications: 15 publications found

Genes affected

CCL17 (HGNC:10615): (C-C motif chemokine ligand 17) 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 T lymphocytes, but not monocytes or granulocytes. The product of this gene binds to chemokine receptors CCR4 and CCR8. This chemokine plays important roles in T cell development in thymus as well as in trafficking and activation of mature T cells. [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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL17	NM_002987.3	c.-59-2410T>C		intron_variant	Intron 1 of 3	ENST00000219244.9	NP_002978.1
CCL17	XM_017023530.2	c.26-2407T>C		intron_variant	Intron 3 of 5		XP_016879019.1
CCL17	XM_011523256.3	c.26-2410T>C		intron_variant	Intron 3 of 5		XP_011521558.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL17	ENST00000219244.9	c.-59-2410T>C		intron_variant	Intron 1 of 3	1	NM_002987.3	ENSP00000219244.4

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116490 AN: 152108 Hom.: 45616 Cov.: 33

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.766 AC: 116596 AN: 152226 Hom.: 45664 Cov.: 33 AF XY: 0.754 AC XY: 56151 AN XY: 74422

African (AFR) AF: 0.913 AC: 37947 AN: 41570

American (AMR) AF: 0.628 AC: 9594 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2687 AN: 3472

East Asian (EAS) AF: 0.533 AC: 2759 AN: 5172

South Asian (SAS) AF: 0.608 AC: 2938 AN: 4830

European-Finnish (FIN) AF: 0.669 AC: 7091 AN: 10602

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51077 AN: 67980

Other (OTH) AF: 0.775 AC: 1635 AN: 2110

Alfa AF: 0.743 Hom.: 26461

Bravo AF: 0.769

Asia WGS AF: 0.600 AC: 2087 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.9
DANN	Benign	0.61
PhyloP100		-0.66
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs223900; hg19: chr16-57445376;