Variant rs2302009 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001371938.1(CCL26):c.*13T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 1,581,242 control chromosomes in the GnomAD database, including 52,309 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 0.29 ( 6810 hom., cov: 32)

Exomes 𝑓: 0.25 ( 45499 hom. )

Consequence

CCL26
NM_001371938.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.696

Variant links:

Genes affected

CCL26 (HGNC:10625): (C-C motif chemokine ligand 26) This gene is one of two Cys-Cys (CC) cytokine genes clustered on the q arm of chromosome 7. 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 normal peripheral blood eosinophils and basophils. This protein also has antimicrobial activity, displaying an antibacterial effect on S. pneumoniae, S. aureus, Non-typeable H. influenzae, and P. aeruginosa. The product of this gene is one of three related chemokines that specifically activate chemokine receptor CCR3. This chemokine may contribute to the eosinophil accumulation in atopic diseases. [provided by RefSeq, Jul 2020]

CCL26 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 (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
CCL26	NM_001371938.1 linkuse as main transcript	c.*13T>G	3_prime_UTR_variant	3/3	ENST00000005180.9	NP_001358867.1
CCL26	NM_001371936.1 linkuse as main transcript	c.*13T>G	3_prime_UTR_variant	4/4		NP_001358865.1
CCL26	NM_006072.4 linkuse as main transcript	c.*13T>G	3_prime_UTR_variant	4/4		NP_006063.1	Q9Y258

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCL26	ENST00000005180.9 linkuse as main transcript	c.*13T>G		3_prime_UTR_variant	3/3	1	NM_001371938.1	ENSP00000005180.4		Q9Y258
CCL26	ENST00000394905.2 linkuse as main transcript	c.*13T>G		3_prime_UTR_variant	4/4	1		ENSP00000378365.2		Q9Y258

Frequencies

GnomAD3 genomes

AF:

0.288

AC:

43720

AN:

152044

Hom.:

6796

Cov.:

show subpopulations

Gnomad AFR

AF:

0.401

Gnomad AMI

AF:

0.261

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.247

Gnomad EAS

AF:

0.116

Gnomad SAS

AF:

0.210

Gnomad FIN

AF:

0.290

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.252

Gnomad OTH

AF:

0.271

GnomAD3 exomes

AF:

0.244

AC:

61138

AN:

250758

Hom.:

7958

AF XY:

0.241

AC XY:

32659

AN XY:

135558

show subpopulations

Gnomad AFR exome

AF:

0.404

Gnomad AMR exome

AF:

0.193

Gnomad ASJ exome

AF:

0.253

Gnomad EAS exome

AF:

0.126

Gnomad SAS exome

AF:

0.219

Gnomad FIN exome

AF:

0.295

Gnomad NFE exome

AF:

0.251

Gnomad OTH exome

AF:

0.253

GnomAD4 exome

AF:

0.248

AC:

354880

AN:

1429080

Hom.:

45499

Cov.:

AF XY:

0.247

AC XY:

176312

AN XY:

713004

show subpopulations

Gnomad4 AFR exome

AF:

0.410

Gnomad4 AMR exome

AF:

0.196

Gnomad4 ASJ exome

AF:

0.250

Gnomad4 EAS exome

AF:

0.103

Gnomad4 SAS exome

AF:

0.223

Gnomad4 FIN exome

AF:

0.297

Gnomad4 NFE exome

AF:

0.250

Gnomad4 OTH exome

AF:

0.253

GnomAD4 genome

AF:

0.288

AC:

43772

AN:

152162

Hom.:

6810

Cov.:

AF XY:

0.285

AC XY:

21181

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.401

Gnomad4 AMR

AF:

0.236

Gnomad4 ASJ

AF:

0.247

Gnomad4 EAS

AF:

0.115

Gnomad4 SAS

AF:

0.210

Gnomad4 FIN

AF:

0.290

Gnomad4 NFE

AF:

0.252

Gnomad4 OTH

AF:

0.269

Alfa

AF:

0.250

Hom.:

9065

Bravo

AF:

0.287

Asia WGS

AF:

0.176

AC:

611

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.9

DANN

Benign

0.70

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