rs2302004

Variant names:

• chr7-75813537-A-G
• rs2302004
• NM_002991.3:c.73+106T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-75813537-A-G
• chr7-75813537-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002991.3(CCL24):​c.73+106T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 1,253,546 control chromosomes in the GnomAD database, including 126,459 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 0.45 (15487 hom., cov: 32)
  • Exomes 𝑓: 0.44 (110972 hom.)
• Consequence: CCL24 NM_002991.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL24	NM_002991.3	c.73+106T>C		intron_variant	Intron 1 of 2	ENST00000222902.7	NP_002982.2
CCL24	NM_001371193.1	c.73+106T>C		intron_variant	Intron 2 of 3		NP_001358122.1
CCL24	XM_011516460.3	c.73+106T>C		intron_variant	Intron 4 of 5		XP_011514762.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL24	ENST00000222902.7	c.73+106T>C		intron_variant	Intron 1 of 2	1	NM_002991.3	ENSP00000222902.2
CCL24	ENST00000416943.1	c.73+106T>C		intron_variant	Intron 2 of 3	1		ENSP00000400533.1

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67838 AN: 151860 Hom.: 15458 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.428

GnomAD4 exome AF: 0.443 AC: 487809 AN: 1101568 Hom.: 110972 Cov.: 15 AF XY: 0.442 AC XY: 247855 AN XY: 561370

African (AFR) AF: 0.424 AC: 11113 AN: 26240

American (AMR) AF: 0.575 AC: 24898 AN: 43334

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 10794 AN: 23442

East Asian (EAS) AF: 0.651 AC: 24452 AN: 37564

South Asian (SAS) AF: 0.445 AC: 34708 AN: 78034

European-Finnish (FIN) AF: 0.495 AC: 26080 AN: 52718

Middle Eastern (MID) AF: 0.419 AC: 1986 AN: 4740

European-Non Finnish (NFE) AF: 0.422 AC: 331854 AN: 787258

Other (OTH) AF: 0.454 AC: 21924 AN: 48238

GnomAD4 genome AF: 0.447 AC: 67910 AN: 151978 Hom.: 15487 Cov.: 32 AF XY: 0.451 AC XY: 33520 AN XY: 74296

African (AFR) AF: 0.423 AC: 17529 AN: 41456

American (AMR) AF: 0.518 AC: 7906 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1625 AN: 3468

East Asian (EAS) AF: 0.676 AC: 3490 AN: 5164

South Asian (SAS) AF: 0.460 AC: 2217 AN: 4824

European-Finnish (FIN) AF: 0.492 AC: 5195 AN: 10568

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28649 AN: 67926

Other (OTH) AF: 0.425 AC: 896 AN: 2110

Alfa AF: 0.428 Hom.: 19133

Bravo AF: 0.450

Asia WGS AF: 0.538 AC: 1873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.48
PhyloP100		0.43
PromoterAI		0.043	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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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Other links and lift over

dbSNP: rs2302004; hg19: chr7-75442855; COSMIC: COSV56116266;