2-227805859-G-A

Position:

• chr2-227805859-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000646475.1(CCL20):​c.-201G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 152,418 control chromosomes in the GnomAD database, including 31,982 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 0.63 (31675 hom., cov: 32)
  • Exomes 𝑓: 0.74 (307 hom.)
• Consequence: CCL20 ENST00000646475.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

CCL20 (HGNC:10619): (C-C motif chemokine ligand 20) 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 protein encoded by this gene displays chemotactic activity for lymphocytes and can repress proliferation of myeloid progenitors. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCL20	ENST00000646475.1	c.-201G>A		5_prime_UTR_variant	1/2			ENSP00000496658

Frequencies

GnomAD3 genomes AF: 0.628 AC: 94963 AN: 151202 Hom.: 31681 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.711

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.656

GnomAD4 exome AF: 0.741 AC: 812 AN: 1096 Hom.: 307 Cov.: 0 AF XY: 0.724 AC XY: 391 AN XY: 540

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.742

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 0.600

GnomAD4 genome AF: 0.628 AC: 94987 AN: 151322 Hom.: 31675 Cov.: 32 AF XY: 0.628 AC XY: 46460 AN XY: 73952

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.656

Alfa AF: 0.665 Hom.: 4172

Bravo AF: 0.606

Asia WGS AF: 0.667 AC: 2320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.86

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10175070; hg19: chr2-228670575;