Genetic Variant CCL1:c.*136G>A (chr17-34360423-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_002981.2(CCL1):c.*136G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0257 in 694,788 control chromosomes in the GnomAD database, including 367 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 0.035 ( 138 hom., cov: 32)

Exomes 𝑓: 0.023 ( 229 hom. )

Consequence

CCL1
NM_002981.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.743

Publications

6 publications found

Variant links:

Genes affected

CCL1 (HGNC:10609): (C-C motif chemokine ligand 1) This antimicrobial gene is one of several chemokine genes clustered on the q-arm of chromosome 17. Chemokines form a superfamily of secreted proteins involved in immunoregulatory and inflammatory processes. The superfamily is divided into four subfamilies based on the arrangement of the N-terminal cysteine residues of the mature peptide. This chemokine, a member of the CC subfamily, is secreted by activated T cells and displays chemotactic activity for monocytes but not for neutrophils. It binds to the chemokine (C-C motif) receptor 8. [provided by RefSeq, Sep 2014]

CCL1 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL1	NM_002981.2 link	c.*136G>A		3_prime_UTR_variant	Exon 3 of 3	ENST00000225842.4	NP_002972.1	P22362

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL1	ENST00000225842.4 link	c.*136G>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_002981.2	ENSP00000225842.3		P22362

Frequencies

GnomAD3 genomes

AF:

0.0347

AC:

5280

AN:

152106

Hom.:

137

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0737

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0159

Gnomad ASJ

AF:

0.0118

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0466

Gnomad FIN

AF:

0.0169

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0217

Gnomad OTH

AF:

0.0259

GnomAD4 exome

AF:

0.0232

AC:

12592

AN:

542564

Hom.:

229

Cov.:

AF XY:

0.0241

AC XY:

7026

AN XY:

291048

show subpopulations

African (AFR)

AF:

0.0743

AC:

1118

AN:

15046

American (AMR)

AF:

0.0120

AC:

339

AN:

28166

Ashkenazi Jewish (ASJ)

AF:

0.0149

AC:

241

AN:

16190

East Asian (EAS)

AF:

0.000120

AC:

AN:

33386

South Asian (SAS)

AF:

0.0480

AC:

2652

AN:

55248

European-Finnish (FIN)

AF:

0.0153

AC:

661

AN:

43114

Middle Eastern (MID)

AF:

0.0228

AC:

AN:

3468

European-Non Finnish (NFE)

AF:

0.0214

AC:

6811

AN:

318652

Other (OTH)

AF:

0.0235

AC:

687

AN:

29294

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

593

1186

1779

2372

2965

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

152

228

304

380

<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:

0.0348

AC:

5290

AN:

152224

Hom.:

138

Cov.:

AF XY:

0.0349

AC XY:

2596

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.0738

AC:

3065

AN:

41536

American (AMR)

AF:

0.0158

AC:

242

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0118

AC:

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5178

South Asian (SAS)

AF:

0.0462

AC:

223

AN:

4824

European-Finnish (FIN)

AF:

0.0169

AC:

179

AN:

10592

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0217

AC:

1479

AN:

68018

Other (OTH)

AF:

0.0256

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

257

514

772

1029

1286

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

180

240

300

<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:

0.0222

Hom.:

Bravo

AF:

0.0362

Asia WGS

AF:

0.0190

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.3

(source)

DANN

Benign

0.23

PhyloP100

0.74

Mutation Taster

=100/0

polymorphism

(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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over