rs7241007

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.31
Variant links:
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]

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ACMG classification

Classification made for transcript

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 rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZNF519ENST00000592345.5 linkn.714-6118T>C intron_variant Intron 4 of 4 3

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7241007; hg19: chr18-14063632; API