rs1719153

Variant names:

• chr17-36105836-A-T
• rs1719153
• NM_002984.4:c.*524A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002984.4(CCL4):​c.*524A>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,158 control chromosomes in the GnomAD database, including 2,792 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 0.18 (2792 hom., cov: 32)
• Consequence: CCL4 NM_002984.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.357
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL4	NM_002984.4	c.*524A>T		downstream_gene_variant		ENST00000615863.2	NP_002975.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL4	ENST00000615863.2	c.*524A>T		downstream_gene_variant		1	NM_002984.4	ENSP00000482259.1
CCL4	ENST00000621626.1	c.*529A>T		downstream_gene_variant		1		ENSP00000480569.1
CCL4	ENST00000613947.1	n.*222A>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26841 AN: 152040 Hom.: 2792 Cov.: 32

Gnomad AFR AF: 0.0692

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.180

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.176 AC: 26845 AN: 152158 Hom.: 2792 Cov.: 32 AF XY: 0.175 AC XY: 12988 AN XY: 74364

African (AFR) AF: 0.0694 AC: 2880 AN: 41504

American (AMR) AF: 0.185 AC: 2828 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 534 AN: 3468

East Asian (EAS) AF: 0.305 AC: 1581 AN: 5178

South Asian (SAS) AF: 0.228 AC: 1100 AN: 4816

European-Finnish (FIN) AF: 0.157 AC: 1662 AN: 10586

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15555 AN: 67996

Other (OTH) AF: 0.178 AC: 375 AN: 2112

Alfa AF: 0.203 Hom.: 420

Bravo AF: 0.177

Asia WGS AF: 0.272 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.8
DANN	Benign	0.85
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs1719153; hg19: chr17-34433229;