chr18-14063633-A-G

Variant names:

• chr18-14063633-A-G
• rs7241007
• ENST00000592345.5:n.714-6118T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000592345.5(ZNF519):​n.714-6118T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ZNF519 ENST00000592345.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 1 publications found

Genes affected

ZNF519 (HGNC:30574): (zinc finger protein 519) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZNF519	ENST00000592345.5	n.714-6118T>C		intron_variant	Intron 4 of 4	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

African (AFR) AF: 0.323 AC: 13402 AN: 41488

American (AMR) AF: 0.181 AC: 2771 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 752 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5188

South Asian (SAS) AF: 0.102 AC: 494 AN: 4824

European-Finnish (FIN) AF: 0.318 AC: 3364 AN: 10580

Middle Eastern (MID) AF: 0.257 AC: 75 AN: 292

European-Non Finnish (NFE) AF: 0.224 AC: 15203 AN: 67988

Other (OTH) AF: 0.227 AC: 479 AN: 2110

Alfa AF: 0.237 Hom.: 611

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7241007; hg19: chr18-14063632;