18-14063633-A-G

Position:

• chr18-14063633-A-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 0.242 in 152,134 control chromosomes in the GnomAD database, including 4,917 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 (4917 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.14063633A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF519	ENST00000592345.5	n.714-6118T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36771 AN: 152016 Hom.: 4912 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.242 AC: 36793 AN: 152134 Hom.: 4917 Cov.: 32 AF XY: 0.240 AC XY: 17851 AN XY: 74390

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.227

Alfa AF: 0.234 Hom.: 573

Bravo AF: 0.234

Asia WGS AF: 0.0800 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7241007; hg19: chr18-14063632;