5-43360163-C-G

Position:

• chr5-43360163-C-G

Variant summary

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

The variant allele was found at a frequency of 0.473 in 151,910 control chromosomes in the GnomAD database, including 17,484 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 0.47 (17484 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.43360163C>G		intergenic_region
CCL28	XR_427660.3	n.519-2491G>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71814 AN: 151792 Hom.: 17497 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.473 AC: 71821 AN: 151910 Hom.: 17484 Cov.: 31 AF XY: 0.470 AC XY: 34909 AN XY: 74202

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.494

Alfa AF: 0.361 Hom.: 969

Bravo AF: 0.467

Asia WGS AF: 0.255 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.0
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11950448; hg19: chr5-43360265;