Variant 7-75813412-T-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_002991.3(CCL24):c.85A>C(p.Ile29Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 1,605,198 control chromosomes in the GnomAD database, including 47,356 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.25 ( 5570 hom., cov: 32)

Exomes 𝑓: 0.22 ( 41786 hom. )

Consequence

CCL24
NM_002991.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.168

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

Computational evidence support a benign effect (MetaRNN=1.69307E-4).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
CCL24	NM_002991.3 linkuse as main transcript	c.85A>C	p.Ile29Leu	missense_variant	2/3	ENST00000222902.7	NP_002982.2
CCL24	NM_001371193.1 linkuse as main transcript	c.85A>C	p.Ile29Leu	missense_variant	3/4		NP_001358122.1
CCL24	XM_011516460.3 linkuse as main transcript	c.85A>C	p.Ile29Leu	missense_variant	5/6		XP_011514762.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCL24	ENST00000222902.7 linkuse as main transcript	c.85A>C	p.Ile29Leu	missense_variant	2/3	1	NM_002991.3	ENSP00000222902	P1
CCL24	ENST00000416943.1 linkuse as main transcript	c.85A>C	p.Ile29Leu	missense_variant	3/4	1		ENSP00000400533	P1

Frequencies

GnomAD3 genomes

AF:

0.253

AC:

38417

AN:

152068

Hom.:

5547

Cov.:

show subpopulations

Gnomad AFR

AF:

0.280

Gnomad AMI

AF:

0.128

Gnomad AMR

AF:

0.377

Gnomad ASJ

AF:

0.282

Gnomad EAS

AF:

0.567

Gnomad SAS

AF:

0.348

Gnomad FIN

AF:

0.167

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.191

Gnomad OTH

AF:

0.259

GnomAD3 exomes

AF:

0.286

AC:

71239

AN:

249118

Hom.:

12806

AF XY:

0.278

AC XY:

37397

AN XY:

134686

show subpopulations

Gnomad AFR exome

AF:

0.282

Gnomad AMR exome

AF:

0.500

Gnomad ASJ exome

AF:

0.278

Gnomad EAS exome

AF:

0.560

Gnomad SAS exome

AF:

0.348

Gnomad FIN exome

AF:

0.160

Gnomad NFE exome

AF:

0.186

Gnomad OTH exome

AF:

0.260

GnomAD4 exome

AF:

0.220

AC:

320328

AN:

1453012

Hom.:

41786

Cov.:

AF XY:

0.223

AC XY:

161139

AN XY:

723198

show subpopulations

Gnomad4 AFR exome

AF:

0.283

Gnomad4 AMR exome

AF:

0.484

Gnomad4 ASJ exome

AF:

0.282

Gnomad4 EAS exome

AF:

0.555

Gnomad4 SAS exome

AF:

0.342

Gnomad4 FIN exome

AF:

0.162

Gnomad4 NFE exome

AF:

0.186

Gnomad4 OTH exome

AF:

0.251

GnomAD4 genome

AF:

0.253

AC:

38467

AN:

152186

Hom.:

5570

Cov.:

AF XY:

0.258

AC XY:

19205

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.280

Gnomad4 AMR

AF:

0.377

Gnomad4 ASJ

AF:

0.282

Gnomad4 EAS

AF:

0.567

Gnomad4 SAS

AF:

0.348

Gnomad4 FIN

AF:

0.167

Gnomad4 NFE

AF:

0.191

Gnomad4 OTH

AF:

0.259

Alfa

AF:

0.220

Hom.:

7790

Bravo

AF:

0.270

TwinsUK

AF:

0.197

AC:

732

ALSPAC

AF:

0.187

AC:

720

ESP6500AA

AF:

0.279

AC:

1230

ESP6500EA

AF:

0.201

AC:

1725

ExAC

AF:

0.276

AC:

33489

Asia WGS

AF:

0.434

AC:

1512

AN:

3478

EpiCase

AF:

0.193

EpiControl

AF:

0.193

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.81

BayesDel_noAF

Benign

-0.79

CADD

Benign

2.5

DANN

Benign

0.68

DEOGEN2

Benign

0.083

T;T

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.17

LIST_S2

Benign

0.39

.;T

MetaRNN

Benign

0.00017

T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

1.2

L;L

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.37

PROVEAN

Benign

-0.79

N;N

REVEL

Benign

0.051

Sift

Benign

0.32

T;T

Sift4G

Benign

0.53

T;T

Polyphen

0.0040

B;B

Vest4

0.064

MPC

0.17

ClinPred

0.0047

GERP RS

-0.41

Varity_R

0.065

gMVP

0.37

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