rs1719144

Variant names:

• chr17-36104010-G-A
• rs1719144
• NM_002984.4:c.76+29G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002984.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL4	NM_002984.4	MANE Select	c.76+29G>A		intron	N/A	NP_002975.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL4	ENST00000615863.2	TSL:1 MANE Select	c.76+29G>A		intron	N/A	ENSP00000482259.1
	CCL4	ENST00000621626.1	TSL:1	c.76+29G>A		intron	N/A	ENSP00000480569.1
	CCL4	ENST00000613947.1	TSL:6	n.170G>A		non_coding_transcript_exon	Exon 1 of 1

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

GnomAD2 exomes AF: 0.209 AC: 52368 AN: 251018 AF XY: 0.211

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 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

African (AFR) AF: 0.0460 AC: 1540 AN: 33460

American (AMR) AF: 0.198 AC: 8855 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 4533 AN: 26128

East Asian (EAS) AF: 0.267 AC: 10590 AN: 39688

South Asian (SAS) AF: 0.217 AC: 18683 AN: 86226

European-Finnish (FIN) AF: 0.163 AC: 8728 AN: 53416

Middle Eastern (MID) AF: 0.175 AC: 1010 AN: 5758

European-Non Finnish (NFE) AF: 0.229 AC: 254502 AN: 1111320

Other (OTH) AF: 0.205 AC: 12382 AN: 60354

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

African (AFR) AF: 0.0520 AC: 2159 AN: 41502

American (AMR) AF: 0.178 AC: 2723 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 539 AN: 3460

East Asian (EAS) AF: 0.302 AC: 1562 AN: 5170

South Asian (SAS) AF: 0.226 AC: 1085 AN: 4810

European-Finnish (FIN) AF: 0.157 AC: 1660 AN: 10558

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.230 AC: 15628 AN: 67944

Other (OTH) AF: 0.167 AC: 352 AN: 2110

Alfa AF: 0.196 Hom.: 599

Bravo AF: 0.170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.59
PhyloP100		0.36
PromoterAI		-0.033	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1719144; hg19: chr17-34431403;