dbSNP rs1719130: CCL3:c.189-138A>G (chr17-36088900-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002983.3(CCL3):c.189-138A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 1,154,466 control chromosomes in the GnomAD database, including 31,079 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 0.22 ( 3726 hom., cov: 32)

Exomes 𝑓: 0.23 ( 27353 hom. )

Consequence

CCL3
NM_002983.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.416

Publications

9 publications found

Variant links:

Genes affected

CCL3 (HGNC:10627): (C-C motif chemokine ligand 3) This locus represents a small inducible cytokine. The encoded protein, also known as macrophage inflammatory protein 1 alpha, plays a role in inflammatory responses through binding to the receptors CCR1, CCR4 and CCR5. Polymorphisms at this locus may be associated with both resistance and susceptibility to infection by human immunodeficiency virus type 1.[provided by RefSeq, Sep 2010]

CCL3 links:

CCL3-AS1 (HGNC:55229): (CCL3 antisense RNA 1)

CCL3-AS1 links:

Genome browser will be placed here

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 = 0.332 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002983.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CCL3	NM_002983.3	MANE Select	c.189-138A>G	intron	N/A	NP_002974.1	P10147
CCL3	NR_168494.1		n.962-138A>G	intron	N/A
CCL3	NR_168495.1		n.172-138A>G	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CCL3	ENST00000613922.2	TSL:1 MANE Select	c.189-138A>G	intron	N/A	ENSP00000477908.1	P10147
CCL3	ENST00000614051.1	TSL:1	n.988-138A>G	intron	N/A
CCL3	ENST00000613928.1	TSL:5	n.804-294A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.216

AC:

32807

AN:

152046

Hom.:

3721

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.341

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.174

Gnomad EAS

AF:

0.346

Gnomad SAS

AF:

0.253

Gnomad FIN

AF:

0.156

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.240

Gnomad OTH

AF:

0.214

GnomAD4 exome

AF:

0.227

AC:

227888

AN:

1002302

Hom.:

27353

AF XY:

0.229

AC XY:

118104

AN XY:

515894

show subpopulations

African (AFR)

AF:

0.168

AC:

4086

AN:

24278

American (AMR)

AF:

0.215

AC:

8490

AN:

39484

Ashkenazi Jewish (ASJ)

AF:

0.191

AC:

4387

AN:

22970

East Asian (EAS)

AF:

0.322

AC:

11672

AN:

36252

South Asian (SAS)

AF:

0.241

AC:

18168

AN:

75542

European-Finnish (FIN)

AF:

0.166

AC:

8602

AN:

51806

Middle Eastern (MID)

AF:

0.205

AC:

702

AN:

3430

European-Non Finnish (NFE)

AF:

0.230

AC:

161798

AN:

703672

Other (OTH)

AF:

0.222

AC:

9983

AN:

44868

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

10095

20190

30285

40380

50475

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4246

8492

12738

16984

21230

<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:

0.216

AC:

32816

AN:

152164

Hom.:

3726

Cov.:

AF XY:

0.213

AC XY:

15857

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.175

AC:

7265

AN:

41512

American (AMR)

AF:

0.204

AC:

3121

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.174

AC:

605

AN:

3470

East Asian (EAS)

AF:

0.345

AC:

1783

AN:

5164

South Asian (SAS)

AF:

0.253

AC:

1220

AN:

4820

European-Finnish (FIN)

AF:

0.156

AC:

1658

AN:

10610

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.240

AC:

16345

AN:

67982

Other (OTH)

AF:

0.212

AC:

447

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1300

2599

3899

5198

6498

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

350

700

1050

1400

1750

<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:

0.226

Hom.:

514

Bravo

AF:

0.220

Asia WGS

AF:

0.317

AC:

1101

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

0.047

(source)

DANN

Benign

0.42

PhyloP100

-0.42

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