chr2-227805859-G-A

Variant names:

• chr2-227805859-G-A
• rs10175070
• ENST00000646475.1:c.-201G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646475.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCL20	ENST00000646475.1		c.-201G>A		5_prime_UTR	Exon 1 of 2	ENSP00000496658.1

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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.742 AC: 801 AN: 1080

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 3 AN: 4

Other (OTH) AF: 0.600 AC: 6 AN: 10

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

African (AFR) AF: 0.375 AC: 15471 AN: 41306

American (AMR) AF: 0.628 AC: 9541 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2655 AN: 3456

East Asian (EAS) AF: 0.809 AC: 4180 AN: 5166

South Asian (SAS) AF: 0.648 AC: 3106 AN: 4796

European-Finnish (FIN) AF: 0.724 AC: 7612 AN: 10518

Middle Eastern (MID) AF: 0.713 AC: 204 AN: 286

European-Non Finnish (NFE) AF: 0.744 AC: 50336 AN: 67618

Other (OTH) AF: 0.656 AC: 1378 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.86
PhyloP100		-1.2
PromoterAI		0.078	Neutral

Splicing

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

Other links and lift over

dbSNP: rs10175070; hg19: chr2-228670575;