rs1719144

Positions:

• chr17-36104010-G-A

Variant summary

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

The NM_002984.4(CCL4):​c.76+29G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 1,613,102 control chromosomes in the GnomAD database, including 39,057 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 0.17 (2742 hom., cov: 31)
  • Exomes 𝑓: 0.22 (36315 hom.)
• Consequence: CCL4 NM_002984.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364

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]

CCL4 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCL4	NM_002984.4	c.76+29G>A		intron_variant		ENST00000615863.2	NP_002975.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCL4	ENST00000615863.2	c.76+29G>A		intron_variant		1	NM_002984.4	ENSP00000482259.1
CCL4	ENST00000621626.1	c.76+29G>A		intron_variant		1		ENSP00000480569.1
CCL4	ENST00000613947.1	n.170G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26032 AN: 151920 Hom.: 2745 Cov.: 31

Gnomad AFR AF: 0.0521

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.169

GnomAD3 exomes AF: 0.209 AC: 52368 AN: 251018 Hom.: 5700 AF XY: 0.211 AC XY: 28628 AN XY: 135656

Gnomad AFR exome AF: 0.0462

Gnomad AMR exome AF: 0.206

Gnomad ASJ exome AF: 0.169

Gnomad EAS exome AF: 0.293

Gnomad SAS exome AF: 0.212

Gnomad FIN exome AF: 0.156

Gnomad NFE exome AF: 0.232

Gnomad OTH exome AF: 0.197

GnomAD4 exome AF: 0.220 AC: 320823 AN: 1461064 Hom.: 36315 Cov.: 32 AF XY: 0.220 AC XY: 159891 AN XY: 726846

Gnomad4 AFR exome AF: 0.0460

Gnomad4 AMR exome AF: 0.198

Gnomad4 ASJ exome AF: 0.173

Gnomad4 EAS exome AF: 0.267

Gnomad4 SAS exome AF: 0.217

Gnomad4 FIN exome AF: 0.163

Gnomad4 NFE exome AF: 0.229

Gnomad4 OTH exome AF: 0.205

GnomAD4 genome AF: 0.171 AC: 26023 AN: 152038 Hom.: 2742 Cov.: 31 AF XY: 0.169 AC XY: 12573 AN XY: 74324

Gnomad4 AFR AF: 0.0520

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.167

Alfa AF: 0.199 Hom.: 593

Bravo AF: 0.170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.59

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: rs1719144; hg19: chr17-34431403;