rs367731450
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The ENST00000301215.8(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
ENST00000301215.8 inframe_deletion
ENST00000301215.8 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]
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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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF526 | NM_133444.3 | c.755_757del | p.Glu252del | inframe_deletion | 3/3 | ENST00000301215.8 | NP_597701.1 | |
ZNF526 | NM_001314033.3 | c.755_757del | p.Glu252del | inframe_deletion | 3/3 | NP_001300962.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF526 | ENST00000301215.8 | c.755_757del | p.Glu252del | inframe_deletion | 3/3 | 1 | NM_133444.3 | ENSP00000301215 | P1 | |
ZNF526 | ENST00000710326.1 | c.755_757del | p.Glu252del | inframe_deletion | 3/3 | ENSP00000518206 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0258 AC: 3925AN: 152062Hom.: 172 Cov.: 32
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GnomAD3 exomes AF: 0.00664 AC: 1668AN: 251200Hom.: 55 AF XY: 0.00497 AC XY: 675AN XY: 135788
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GnomAD4 exome AF: 0.00264 AC: 3864AN: 1461862Hom.: 120 AF XY: 0.00235 AC XY: 1711AN XY: 727222
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GnomAD4 genome AF: 0.0259 AC: 3934AN: 152180Hom.: 172 Cov.: 32 AF XY: 0.0246 AC XY: 1833AN XY: 74392
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
ZNF526-related disorder Benign:1
Benign, no assertion criteria provided | 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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at