Variant chr7-75813441-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000222902.7(CCL24):c.74-18C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 1,555,160 control chromosomes in the GnomAD database, including 53,564 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. There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.26 ( 5841 hom., cov: 32)

Exomes 𝑓: 0.24 ( 47723 hom. )

Consequence

CCL24
ENST00000222902.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0190

Variant links:

Genes affected

CCL24 (HGNC:10623): (C-C motif chemokine ligand 24) This gene belongs to the subfamily of small cytokine CC genes. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The CC cytokines are proteins characterized by two adjacent cysteines. The cytokine encoded by this gene displays chemotactic activity on resting T lymphocytes, a minimal activity on neutrophils, and is negative on monocytes and activated T lymphocytes. This protein also has antimicrobial activity, displaying an antibacterial effect on S. pneumoniae, S. aureus, Non-typeable H. influenzae, and P. aeruginosa. Finally, the protein is a strong suppressor of colony formation by a multipotential hematopoietic progenitor cell line. [provided by RefSeq, Jul 2020]

CCL24 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

This place is a probable branch point but likely benign (scored 3 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
CCL24	NM_002991.3 linkuse as main transcript	c.74-18C>T	intron_variant	ENST00000222902.7	NP_002982.2
CCL24	NM_001371193.1 linkuse as main transcript	c.74-18C>T	intron_variant		NP_001358122.1
CCL24	XM_011516460.3 linkuse as main transcript	c.74-18C>T	intron_variant		XP_011514762.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCL24	ENST00000222902.7 linkuse as main transcript	c.74-18C>T		intron_variant		1	NM_002991.3	ENSP00000222902	P1
CCL24	ENST00000416943.1 linkuse as main transcript	c.74-18C>T		intron_variant		1		ENSP00000400533	P1

Frequencies

GnomAD3 genomes

AF:

0.259

AC:

39405

AN:

152008

Hom.:

5827

Cov.:

show subpopulations

Gnomad AFR

AF:

0.242

Gnomad AMI

AF:

0.226

Gnomad AMR

AF:

0.381

Gnomad ASJ

AF:

0.296

Gnomad EAS

AF:

0.638

Gnomad SAS

AF:

0.326

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.215

Gnomad OTH

AF:

0.268

GnomAD3 exomes

AF:

0.305

AC:

75479

AN:

247764

Hom.:

14079

AF XY:

0.294

AC XY:

39384

AN XY:

134008

show subpopulations

Gnomad AFR exome

AF:

0.240

Gnomad AMR exome

AF:

0.500

Gnomad ASJ exome

AF:

0.299

Gnomad EAS exome

AF:

0.652

Gnomad SAS exome

AF:

0.308

Gnomad FIN exome

AF:

0.216

Gnomad NFE exome

AF:

0.216

Gnomad OTH exome

AF:

0.289

GnomAD4 exome

AF:

0.244

AC:

342934

AN:

1403034

Hom.:

47723

Cov.:

AF XY:

0.245

AC XY:

171757

AN XY:

701210

show subpopulations

Gnomad4 AFR exome

AF:

0.244

Gnomad4 AMR exome

AF:

0.487

Gnomad4 ASJ exome

AF:

0.297

Gnomad4 EAS exome

AF:

0.626

Gnomad4 SAS exome

AF:

0.307

Gnomad4 FIN exome

AF:

0.216

Gnomad4 NFE exome

AF:

0.214

Gnomad4 OTH exome

AF:

0.271

GnomAD4 genome

AF:

0.259

AC:

39435

AN:

152126

Hom.:

5841

Cov.:

AF XY:

0.264

AC XY:

19655

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.242

Gnomad4 AMR

AF:

0.382

Gnomad4 ASJ

AF:

0.296

Gnomad4 EAS

AF:

0.637

Gnomad4 SAS

AF:

0.327

Gnomad4 FIN

AF:

0.209

Gnomad4 NFE

AF:

0.215

Gnomad4 OTH

AF:

0.265

Alfa

AF:

0.232

Hom.:

3182

Bravo

AF:

0.276

Asia WGS

AF:

0.439

AC:

1530

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.6

DANN

Benign

0.66

BranchPoint Hunter

3.0

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over