rs11951515

Variant names:

• chr5-43382756-T-C
• rs11951515
• NM_148672.3:c.192-704A>G

Variant summary

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

The NM_148672.3(CCL28):​c.192-704A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,072 control chromosomes in the GnomAD database, including 22,054 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 0.53 (22054 hom., cov: 32)
• Consequence: CCL28 NM_148672.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 7 publications found

Genes affected

CCL28 (HGNC:17700): (C-C motif chemokine ligand 28) This antimicrobial 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 for resting CD4 or CD8 T cells and eosinophils. The product of this gene binds to chemokine receptors CCR3 and CCR10. This chemokine may play a role in the physiology of extracutaneous epithelial tissues, including diverse mucosal organs. Multiple transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Sep 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_148672.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL28	NM_148672.3	MANE Select	c.192-704A>G		intron	N/A	NP_683513.1
	CCL28	NM_001301873.2		c.192-704A>G		intron	N/A	NP_001288802.1
	CCL28	NM_001301874.2		c.192-704A>G		intron	N/A	NP_001288803.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL28	ENST00000361115.4	TSL:1 MANE Select	c.192-704A>G		intron	N/A	ENSP00000354416.4
	CCL28	ENST00000513525.1	TSL:1	c.51-704A>G		intron	N/A	ENSP00000422369.1
	CCL28	ENST00000489442.5	TSL:1	n.192-704A>G		intron	N/A	ENSP00000426424.1

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80441 AN: 151954 Hom.: 22060 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.529 AC: 80449 AN: 152072 Hom.: 22054 Cov.: 32 AF XY: 0.525 AC XY: 39019 AN XY: 74364

African (AFR) AF: 0.504 AC: 20906 AN: 41468

American (AMR) AF: 0.455 AC: 6939 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2063 AN: 3472

East Asian (EAS) AF: 0.156 AC: 808 AN: 5188

South Asian (SAS) AF: 0.414 AC: 1994 AN: 4816

European-Finnish (FIN) AF: 0.582 AC: 6163 AN: 10584

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39819 AN: 67972

Other (OTH) AF: 0.555 AC: 1170 AN: 2108

Alfa AF: 0.543 Hom.: 14718

Bravo AF: 0.516

Asia WGS AF: 0.277 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.0
DANN	Benign	0.88
PhyloP100		-0.056
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: rs11951515; hg19: chr5-43382858;