17-35976530-T-C

Variant names:

• chr17-35976530-T-C
• rs2063979
• NM_004590.4:c.*1036A>G

Variant summary

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

The NM_004590.4(CCL16):​c.*1036A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,996 control chromosomes in the GnomAD database, including 20,091 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 0.46 (20090 hom., cov: 31)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: CCL16 NM_004590.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL16	NM_004590.4	c.*1036A>G		3_prime_UTR_variant	Exon 3 of 3	ENST00000611905.2	NP_004581.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL16	ENST00000611905	c.*1036A>G		3_prime_UTR_variant	Exon 3 of 3	1	NM_004590.4	ENSP00000478024.1
CCL16	ENST00000613642.4	n.*363A>G		non_coding_transcript_exon_variant	Exon 3 of 3	3		ENSP00000478592.1
CCL16	ENST00000613642.4	n.*363A>G		3_prime_UTR_variant	Exon 3 of 3	3		ENSP00000478592.1
CCL16	ENST00000610493.1	n.*1469A>G		downstream_gene_variant		5		ENSP00000478934.1

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70012 AN: 151874 Hom.: 20037 Cov.: 31

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.411

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.461 AC: 70128 AN: 151992 Hom.: 20090 Cov.: 31 AF XY: 0.463 AC XY: 34380 AN XY: 74280

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.413

Alfa AF: 0.327 Hom.: 17910

Bravo AF: 0.494

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.6

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2063979; hg19: chr17-34303566;