chr17-35978128-A-C

Variant names:

• chr17-35978128-A-C
• rs11080369
• NM_004590.4:c.197+15T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

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]

ENSG00000270240 (HGNC:58767):

ENSG00000302706 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004590.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL16	NM_004590.4	MANE Select	c.197+15T>G		intron	N/A	NP_004581.1	O15467

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL16	ENST00000611905.2	TSL:1 MANE Select	c.197+15T>G		intron	N/A	ENSP00000478024.1	O15467
	CCL16	ENST00000890729.1		c.218+15T>G		intron	N/A	ENSP00000560788.1
	CCL16	ENST00000890728.1		c.194+15T>G		intron	N/A	ENSP00000560787.1

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

GnomAD2 exomes AF: 0.0837 AC: 21046 AN: 251418 AF XY: 0.0769

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 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

African (AFR) AF: 0.140 AC: 4688 AN: 33474

American (AMR) AF: 0.178 AC: 7943 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.0406 AC: 1061 AN: 26134

East Asian (EAS) AF: 0.0526 AC: 2088 AN: 39700

South Asian (SAS) AF: 0.0533 AC: 4599 AN: 86258

European-Finnish (FIN) AF: 0.0490 AC: 2618 AN: 53416

Middle Eastern (MID) AF: 0.0718 AC: 414 AN: 5768

European-Non Finnish (NFE) AF: 0.0722 AC: 80326 AN: 1111916

Other (OTH) AF: 0.0733 AC: 4428 AN: 60390

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

African (AFR) AF: 0.142 AC: 5914 AN: 41514

American (AMR) AF: 0.137 AC: 2094 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0421 AC: 146 AN: 3470

East Asian (EAS) AF: 0.0632 AC: 327 AN: 5176

South Asian (SAS) AF: 0.0557 AC: 268 AN: 4814

European-Finnish (FIN) AF: 0.0512 AC: 542 AN: 10592

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.0685 AC: 4657 AN: 68008

Other (OTH) AF: 0.0822 AC: 174 AN: 2116

Alfa AF: 0.0769 Hom.: 1506

Bravo AF: 0.103

Asia WGS AF: 0.0790 AC: 274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.65
PhyloP100		-0.46
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11080369; hg19: chr17-34305164;