rs854692

chr17-35996908-C-T

Variant summary

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

The NR_027922.3(CCL15-CCL14):n.934+813G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,100 control chromosomes in the GnomAD database, including 17,227 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 0.40 (17225 hom., cov: 32)
  • Exomes 𝑓: 0.23 (2 hom.)
• Consequence: CCL15-CCL14 NR_027922.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

Genes affected

CCL15-CCL14 (HGNC:):

CCL15 (HGNC:10613): (C-C motif chemokine ligand 15) This gene is located in a cluster of similar genes in the same region of chromosome 17. These genes encode CC cytokines, which are secreted proteins characterized by two adjacent cysteines. The product of this gene is chemotactic for T cells and monocytes, and acts through C-C chemokine receptor type 1 (CCR1). The proprotein is further processed into numerous smaller functional peptides. Naturally-occurring readthrough transcripts occur from this gene into the downstream gene, CCL14 (chemokine (C-C motif) ligand 14). [provided by RefSeq, Jan 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCL15-CCL14	NR_027922.3	n.934+813G>A		intron_variant, non_coding_transcript_variant
CCL15-CCL14	NR_027921.3	n.934+813G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCL15	ENST00000614368.1	c.*65G>A		3_prime_UTR_variant	3/3	3

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60664 AN: 151892 Hom.: 17179 Cov.: 32

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.337

GnomAD4 exome AF: 0.233 AC: 21 AN: 90 Hom.: 2 Cov.: 0 AF XY: 0.250 AC XY: 19 AN XY: 76

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.205

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.400 AC: 60762 AN: 152010 Hom.: 17225 Cov.: 32 AF XY: 0.402 AC XY: 29885 AN XY: 74274

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.337

Alfa AF: 0.235 Hom.: 9801

Bravo AF: 0.417

Asia WGS AF: 0.458 AC: 1591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.1
Dann	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs854692; hg19: chr17-34323944;