Variant chr7-75772100-G-A 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.73+4C>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 1,586,878 control chromosomes in the GnomAD database, including 33,940 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 0.21 ( 3664 hom., cov: 32)

Exomes 𝑓: 0.20 ( 30276 hom. )

Consequence

CCL26
NM_001371938.1 splice_donor_region, intron

Scores

Splicing: ADA: 0.0007954

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.912

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=-0.78).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
CCL26	NM_001371938.1 linkuse as main transcript	c.73+4C>T	splice_donor_region_variant, intron_variant	ENST00000005180.9
CCL26	NM_001371936.1 linkuse as main transcript	c.73+4C>T	splice_donor_region_variant, intron_variant
CCL26	NM_006072.4 linkuse as main transcript	c.73+4C>T	splice_donor_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCL26	ENST00000005180.9 linkuse as main transcript	c.73+4C>T		splice_donor_region_variant, intron_variant		1	NM_001371938.1	P1
CCL26	ENST00000394905.2 linkuse as main transcript	c.73+4C>T		splice_donor_region_variant, intron_variant		1		P1

Frequencies

GnomAD3 genomes

AF:

0.209

AC:

31757

AN:

152010

Hom.:

3651

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.349

Gnomad ASJ

AF:

0.119

Gnomad EAS

AF:

0.292

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.187

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.182

Gnomad OTH

AF:

0.219

GnomAD3 exomes

AF:

0.234

AC:

48317

AN:

206616

Hom.:

6736

AF XY:

0.225

AC XY:

24978

AN XY:

111068

show subpopulations

Gnomad AFR exome

AF:

0.202

Gnomad AMR exome

AF:

0.472

Gnomad ASJ exome

AF:

0.129

Gnomad EAS exome

AF:

0.286

Gnomad SAS exome

AF:

0.188

Gnomad FIN exome

AF:

0.176

Gnomad NFE exome

AF:

0.191

Gnomad OTH exome

AF:

0.222

GnomAD4 exome

AF:

0.197

AC:

283362

AN:

1434750

Hom.:

30276

Cov.:

AF XY:

0.196

AC XY:

139735

AN XY:

711840

show subpopulations

Gnomad4 AFR exome

AF:

0.202

Gnomad4 AMR exome

AF:

0.454

Gnomad4 ASJ exome

AF:

0.129

Gnomad4 EAS exome

AF:

0.309

Gnomad4 SAS exome

AF:

0.189

Gnomad4 FIN exome

AF:

0.173

Gnomad4 NFE exome

AF:

0.188

Gnomad4 OTH exome

AF:

0.198

GnomAD4 genome

AF:

0.209

AC:

31787

AN:

152128

Hom.:

3664

Cov.:

AF XY:

0.212

AC XY:

15793

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.202

Gnomad4 AMR

AF:

0.350

Gnomad4 ASJ

AF:

0.119

Gnomad4 EAS

AF:

0.293

Gnomad4 SAS

AF:

0.201

Gnomad4 FIN

AF:

0.187

Gnomad4 NFE

AF:

0.182

Gnomad4 OTH

AF:

0.218

Alfa

AF:

0.191

Hom.:

4866

Bravo

AF:

0.230

Asia WGS

AF:

0.250

AC:

869

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.034

DANN

Benign

0.79

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00080

dbscSNV1_RF

Benign

0.0080

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