NM_002984.4:c.192-215C>A

Variant names:

• chr17-36105010-C-A
• rs1634517
• NM_002984.4:c.192-215C>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.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
• Publications: 14 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 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.192-215C>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.192-215C>A		intron	N/A	ENSP00000482259.1
	CCL4	ENST00000621626.1	TSL:1	c.77-215C>A		intron	N/A	ENSP00000480569.1
	CCL4	ENST00000613947.1	TSL:6	n.1170C>A		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.234 AC: 3751 AN: 16010

American (AMR) AF: 0.223 AC: 7746 AN: 34780

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 3912 AN: 20074

East Asian (EAS) AF: 0.269 AC: 8654 AN: 32172

South Asian (SAS) AF: 0.247 AC: 15575 AN: 63000

European-Finnish (FIN) AF: 0.171 AC: 7803 AN: 45746

Middle Eastern (MID) AF: 0.219 AC: 879 AN: 4014

European-Non Finnish (NFE) AF: 0.245 AC: 79387 AN: 324682

Other (OTH) AF: 0.237 AC: 7337 AN: 30978

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

African (AFR) AF: 0.236 AC: 9786 AN: 41408

American (AMR) AF: 0.215 AC: 3278 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3468

East Asian (EAS) AF: 0.315 AC: 1627 AN: 5168

South Asian (SAS) AF: 0.255 AC: 1229 AN: 4814

European-Finnish (FIN) AF: 0.164 AC: 1737 AN: 10588

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16506 AN: 67936

Other (OTH) AF: 0.228 AC: 479 AN: 2104

Alfa AF: 0.247 Hom.: 1383

Bravo AF: 0.241

Asia WGS AF: 0.313 AC: 1087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.31
DANN	Benign	0.35
PhyloP100		-1.5
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: rs1634517; hg19: chr17-34432403;