chr17-35978128-A-C

Position:

• chr17-35978128-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004590.4(CCL16):​c.197+15T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0758 in 1,613,960 control chromosomes in the GnomAD database, including 5,258 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 0.093 (771 hom., cov: 32)
  • Exomes 𝑓: 0.074 (4487 hom.)
• Consequence: CCL16 NM_004590.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.459

Genes affected

CCL16 (HGNC:10614): (C-C motif chemokine ligand 16) This gene is one of several cytokine genes clustered on the q-arm of chromosome 17. 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 lymphocytes and monocytes but not for neutrophils. This cytokine also shows a potent myelosuppressive activity and suppresses proliferation of myeloid progenitor cells. The expression of this gene is upregulated by IL-10. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCL16	NM_004590.4	c.197+15T>G		intron_variant		ENST00000611905.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCL16	ENST00000611905.2	c.197+15T>G		intron_variant		1	NM_004590.4	P1
CCL16	ENST00000610493.1	c.*267+15T>G		intron_variant, NMD_transcript_variant		5
CCL16	ENST00000613642.4	c.121+15T>G		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0931 AC: 14151 AN: 152064 Hom.: 767 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.0636

Gnomad SAS AF: 0.0552

Gnomad FIN AF: 0.0512

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0685

Gnomad OTH AF: 0.0798

GnomAD3 exomes AF: 0.0837 AC: 21046 AN: 251418 Hom.: 1179 AF XY: 0.0769 AC XY: 10455 AN XY: 135886

Gnomad AFR exome AF: 0.143

Gnomad AMR exome AF: 0.184

Gnomad ASJ exome AF: 0.0435

Gnomad EAS exome AF: 0.0594

Gnomad SAS exome AF: 0.0510

Gnomad FIN exome AF: 0.0498

Gnomad NFE exome AF: 0.0684

Gnomad OTH exome AF: 0.0670

GnomAD4 exome AF: 0.0740 AC: 108165 AN: 1461778 Hom.: 4487 Cov.: 32 AF XY: 0.0723 AC XY: 52603 AN XY: 727202

Gnomad4 AFR exome AF: 0.140

Gnomad4 AMR exome AF: 0.178

Gnomad4 ASJ exome AF: 0.0406

Gnomad4 EAS exome AF: 0.0526

Gnomad4 SAS exome AF: 0.0533

Gnomad4 FIN exome AF: 0.0490

Gnomad4 NFE exome AF: 0.0722

Gnomad4 OTH exome AF: 0.0733

GnomAD4 genome AF: 0.0931 AC: 14168 AN: 152182 Hom.: 771 Cov.: 32 AF XY: 0.0937 AC XY: 6973 AN XY: 74402

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.0632

Gnomad4 SAS AF: 0.0557

Gnomad4 FIN AF: 0.0512

Gnomad4 NFE AF: 0.0685

Gnomad4 OTH AF: 0.0822

Alfa AF: 0.0733 Hom.: 636

Bravo AF: 0.103

Asia WGS AF: 0.0790 AC: 274 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	1.6
DANN	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11080369; hg19: chr17-34305164;