7-75812196-C-T

Variant names:

• chr7-75812196-C-T
• rs11465310
• NM_002991.3:c.192-232G>A

Variant summary

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

The NM_002991.3(CCL24):​c.192-232G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 151,882 control chromosomes in the GnomAD database, including 1,125 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 0.11 (1125 hom., cov: 29)
• Consequence: CCL24 NM_002991.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.51
• Publications: 0 publications found

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 = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCL24	NM_002991.3	c.192-232G>A		intron_variant	Intron 2 of 2	ENST00000222902.7	NP_002982.2
CCL24	NM_001371193.1	c.192-232G>A		intron_variant	Intron 3 of 3		NP_001358122.1
CCL24	XM_011516460.3	c.192-232G>A		intron_variant	Intron 5 of 5		XP_011514762.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCL24	ENST00000222902.7	c.192-232G>A		intron_variant	Intron 2 of 2	1	NM_002991.3	ENSP00000222902.2
CCL24	ENST00000416943.1	c.192-232G>A		intron_variant	Intron 3 of 3	1		ENSP00000400533.1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16447 AN: 151764 Hom.: 1125 Cov.: 29

Gnomad AFR AF: 0.0361

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.0973

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.113

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.108 AC: 16450 AN: 151882 Hom.: 1125 Cov.: 29 AF XY: 0.108 AC XY: 8040 AN XY: 74224

African (AFR) AF: 0.0361 AC: 1495 AN: 41460

American (AMR) AF: 0.0972 AC: 1479 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 496 AN: 3468

East Asian (EAS) AF: 0.171 AC: 880 AN: 5150

South Asian (SAS) AF: 0.132 AC: 632 AN: 4794

European-Finnish (FIN) AF: 0.139 AC: 1469 AN: 10548

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.141 AC: 9561 AN: 67950

Other (OTH) AF: 0.112 AC: 236 AN: 2104

Alfa AF: 0.0577 Hom.: 52

Bravo AF: 0.104

Asia WGS AF: 0.125 AC: 435 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	0.61
DANN	Benign	0.40
PhyloP100		-2.5
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

Other links and lift over

dbSNP: rs11465310; hg19: chr7-75441514;