rs367731450
Positions:
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_133444.3(ZNF526):βc.755_757delβ(p.Glu252del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00483 in 1,614,042 control chromosomes in the GnomAD database, including 292 homozygotes. Variant has been reported in ClinVar as Benign (β β ).
Frequency
Genomes: π 0.026 ( 172 hom., cov: 32)
Exomes π: 0.0026 ( 120 hom. )
Consequence
ZNF526
NM_133444.3 inframe_deletion
NM_133444.3 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.46
Genes affected
ZNF526 (HGNC:29415): (zinc finger protein 526) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 19-42225153-TGAG-T is Benign according to our data. Variant chr19-42225153-TGAG-T is described in ClinVar as [Benign]. Clinvar id is 212686.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0867 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF526 | NM_133444.3 | c.755_757del | p.Glu252del | inframe_deletion | 3/3 | ENST00000301215.8 | |
ZNF526 | NM_001314033.3 | c.755_757del | p.Glu252del | inframe_deletion | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF526 | ENST00000301215.8 | c.755_757del | p.Glu252del | inframe_deletion | 3/3 | 1 | NM_133444.3 | P1 | |
ZNF526 | ENST00000710326.1 | c.755_757del | p.Glu252del | inframe_deletion | 3/3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0258 AC: 3925AN: 152062Hom.: 172 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
3925
AN:
152062
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00664 AC: 1668AN: 251200Hom.: 55 AF XY: 0.00497 AC XY: 675AN XY: 135788
GnomAD3 exomes
AF:
AC:
1668
AN:
251200
Hom.:
AF XY:
AC XY:
675
AN XY:
135788
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00264 AC: 3864AN: 1461862Hom.: 120 AF XY: 0.00235 AC XY: 1711AN XY: 727222
GnomAD4 exome
AF:
AC:
3864
AN:
1461862
Hom.:
AF XY:
AC XY:
1711
AN XY:
727222
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0259 AC: 3934AN: 152180Hom.: 172 Cov.: 32 AF XY: 0.0246 AC XY: 1833AN XY: 74392
GnomAD4 genome
?
AF:
AC:
3934
AN:
152180
Hom.:
Cov.:
32
AF XY:
AC XY:
1833
AN XY:
74392
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
15
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 16, 2013 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
ZNF526-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 07, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at