Genetic Variant CCL4:c.191+90A>G (chr17-36104732-A-G) – 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.191+90A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 1,535,036 control chromosomes in the GnomAD database, including 453,608 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 0.76 ( 44684 hom., cov: 31)

Exomes 𝑓: 0.77 ( 408924 hom. )

Consequence

CCL4
NM_002984.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0820

Publications

15 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 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.191+90A>G		intron	N/A	NP_002975.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CCL4	ENST00000615863.2	TSL:1 MANE Select	c.191+90A>G	intron	N/A	ENSP00000482259.1
CCL4	ENST00000621626.1	TSL:1	c.77-493A>G	intron	N/A	ENSP00000480569.1
CCL4	ENST00000613947.1	TSL:6	n.892A>G	non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.765

AC:

116182

AN:

151944

Hom.:

44641

Cov.:

show subpopulations

Gnomad AFR

AF:

0.722

Gnomad AMI

AF:

0.807

Gnomad AMR

AF:

0.838

Gnomad ASJ

AF:

0.748

Gnomad EAS

AF:

0.935

Gnomad SAS

AF:

0.713

Gnomad FIN

AF:

0.773

Gnomad MID

AF:

0.766

Gnomad NFE

AF:

0.763

Gnomad OTH

AF:

0.777

GnomAD4 exome

AF:

0.768

AC:

1061573

AN:

1382974

Hom.:

408924

Cov.:

AF XY:

0.765

AC XY:

526869

AN XY:

688822

show subpopulations

African (AFR)

AF:

0.726

AC:

23201

AN:

31942

American (AMR)

AF:

0.879

AC:

35074

AN:

39916

Ashkenazi Jewish (ASJ)

AF:

0.762

AC:

19210

AN:

25220

East Asian (EAS)

AF:

0.950

AC:

36718

AN:

38648

South Asian (SAS)

AF:

0.708

AC:

58574

AN:

82760

European-Finnish (FIN)

AF:

0.765

AC:

39744

AN:

51952

Middle Eastern (MID)

AF:

0.723

AC:

3851

AN:

5326

European-Non Finnish (NFE)

AF:

0.763

AC:

801008

AN:

1049580

Other (OTH)

AF:

0.767

AC:

44193

AN:

57630

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

12849

25697

38546

51394

64243

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19120

38240

57360

76480

95600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.765

AC:

116282

AN:

152062

Hom.:

44684

Cov.:

AF XY:

0.765

AC XY:

56891

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.722

AC:

29945

AN:

41454

American (AMR)

AF:

0.839

AC:

12826

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.748

AC:

2596

AN:

3472

East Asian (EAS)

AF:

0.935

AC:

4820

AN:

5156

South Asian (SAS)

AF:

0.713

AC:

3437

AN:

4818

European-Finnish (FIN)

AF:

0.773

AC:

8198

AN:

10600

Middle Eastern (MID)

AF:

0.762

AC:

224

AN:

294

European-Non Finnish (NFE)

AF:

0.763

AC:

51859

AN:

67954

Other (OTH)

AF:

0.778

AC:

1641

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1439

2877

4316

5754

7193

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

860

1720

2580

3440

4300

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.759

Hom.:

34691

Bravo

AF:

0.772

Asia WGS

AF:

0.847

AC:

2942

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.6

(source)

DANN

Benign

0.44

PhyloP100

0.082

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over