rs1634517

chr17-36105010-C-A

Variant summary

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

The NM_002984.4(CCL4):c.192-215C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 723,424 control chromosomes in the GnomAD database, including 20,638 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 0.23 (4228 hom., cov: 31)
  • Exomes 𝑓: 0.24 (16410 hom.)
• Consequence: CCL4 NM_002984.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

CCL4 (HGNC:10630): (C-C motif chemokine ligand 4) The protein encoded by this gene is a mitogen-inducible monokine and is one of the major HIV-suppressive factors produced by CD8+ T-cells. The encoded protein is secreted and has chemokinetic and inflammatory functions. [provided by RefSeq, Dec 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCL4	NM_002984.4	c.192-215C>A		intron_variant		ENST00000615863.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCL4	ENST00000615863.2	c.192-215C>A		intron_variant		1	NM_002984.4	P1
CCL4	ENST00000621626.1	c.77-215C>A		intron_variant		1
CCL4	ENST00000613947.1	n.1170C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35620 AN: 151850 Hom.: 4221 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.231

GnomAD4 exome AF: 0.236 AC: 135044 AN: 571456 Hom.: 16410 Cov.: 5 AF XY: 0.238 AC XY: 73283 AN XY: 308426

Gnomad4 AFR exome AF: 0.234

Gnomad4 AMR exome AF: 0.223

Gnomad4 ASJ exome AF: 0.195

Gnomad4 EAS exome AF: 0.269

Gnomad4 SAS exome AF: 0.247

Gnomad4 FIN exome AF: 0.171

Gnomad4 NFE exome AF: 0.245

Gnomad4 OTH exome AF: 0.237

GnomAD4 genome AF: 0.235 AC: 35640 AN: 151968 Hom.: 4228 Cov.: 31 AF XY: 0.232 AC XY: 17206 AN XY: 74300

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.228

Alfa AF: 0.237 Hom.: 538

Bravo AF: 0.241

Asia WGS AF: 0.313 AC: 1087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.31
Dann	Benign	0.35

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

Publications

LitVar

Other links and lift over

dbSNP: rs1634517; hg19: chr17-34432403;