rs6749704

chr2-227813126-T-C

Variant summary

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

The ENST00000646475.1(CCL20):c.-90-696T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,116 control chromosomes in the GnomAD database, including 4,529 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 0.24 (4529 hom., cov: 32)
• Consequence: CCL20 ENST00000646475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCL20	ENST00000646475.1	c.-90-696T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36250 AN: 151998 Hom.: 4523 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.238 AC: 36268 AN: 152116 Hom.: 4529 Cov.: 32 AF XY: 0.235 AC XY: 17476 AN XY: 74350

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.246

Alfa AF: 0.268 Hom.: 5673

Bravo AF: 0.241

Asia WGS AF: 0.227 AC: 793 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	2.6
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6749704; hg19: chr2-228677842;