chr16-57405676-G-A

Variant names:

• chr16-57405676-G-A
• rs11076191
• NM_002987.3:c.-60+840G>A

Variant summary

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

The NM_002987.3(CCL17):​c.-60+840G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,044 control chromosomes in the GnomAD database, including 1,631 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 0.13 (1631 hom., cov: 31)
• Consequence: CCL17 NM_002987.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL17	NM_002987.3	c.-60+840G>A		intron_variant	Intron 1 of 3	ENST00000219244.9	NP_002978.1
CCL17	XM_017023530.2	c.25+840G>A		intron_variant	Intron 3 of 5		XP_016879019.1
CCL17	XM_011523256.3	c.25+840G>A		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.-60+840G>A		intron_variant	Intron 1 of 3	1	NM_002987.3	ENSP00000219244.4

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19454 AN: 151926 Hom.: 1633 Cov.: 31

Gnomad AFR AF: 0.0328

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0753

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.128 AC: 19447 AN: 152044 Hom.: 1631 Cov.: 31 AF XY: 0.131 AC XY: 9701 AN XY: 74296

African (AFR) AF: 0.0327 AC: 1356 AN: 41506

American (AMR) AF: 0.112 AC: 1712 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 574 AN: 3466

East Asian (EAS) AF: 0.0755 AC: 391 AN: 5178

South Asian (SAS) AF: 0.199 AC: 956 AN: 4806

European-Finnish (FIN) AF: 0.218 AC: 2304 AN: 10562

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11753 AN: 67950

Other (OTH) AF: 0.125 AC: 263 AN: 2108

Alfa AF: 0.151 Hom.: 1239

Bravo AF: 0.115

Asia WGS AF: 0.100 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.97
DANN	Benign	0.39
PhyloP100		0.10
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: rs11076191; hg19: chr16-57439588;