Genetic Variant NM_002984.4:c.76+29G>A (chr17-36104010-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.364

Publications

5 publications found

Variant links:

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 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL4	NM_002984.4 link	c.76+29G>A		intron_variant	Intron 1 of 2	ENST00000615863.2	NP_002975.1	P13236

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CCL4	ENST00000615863.2 link	c.76+29G>A	intron_variant	Intron 1 of 2	1	NM_002984.4	ENSP00000482259.1	P13236
CCL4	ENST00000621626.1 link	c.76+29G>A	intron_variant	Intron 1 of 1	1		ENSP00000480569.1	Q7M4M2
CCL4	ENST00000613947.1 link	n.170G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

26032

AN:

151920

Hom.:

2745

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.220

AC XY:

159891

AN XY:

726846

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

14292

28584

42877

57169

71461

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.171

AC:

26023

AN:

152038

Hom.:

2742

Cov.:

AF XY:

0.169

AC XY:

12573

AN XY:

74324

show subpopulations

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:

AN:

292

European-Non Finnish (NFE)

AF:

0.230

AC:

15628

AN:

67944

Other (OTH)

AF:

0.167

AC:

352

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1054

2109

3163

4218

5272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.196

Hom.:

599

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

(source)

DANN

Benign

0.59

PhyloP100

0.36

PromoterAI

-0.033

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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NM_002984.4:c.76+29G>A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over