chr19-42224684-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_133444.3(ZNF526):c.281T>C(p.Val94Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 1,614,138 control chromosomes in the GnomAD database, including 9,141 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_133444.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF526 | NM_133444.3 | c.281T>C | p.Val94Ala | missense_variant | 3/3 | ENST00000301215.8 | |
ZNF526 | NM_001314033.3 | c.281T>C | p.Val94Ala | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF526 | ENST00000301215.8 | c.281T>C | p.Val94Ala | missense_variant | 3/3 | 1 | NM_133444.3 | P1 | |
ZNF526 | ENST00000710326.1 | c.281T>C | p.Val94Ala | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0791 AC: 12042AN: 152156Hom.: 665 Cov.: 32
GnomAD3 exomes AF: 0.109 AC: 27336AN: 251264Hom.: 1738 AF XY: 0.114 AC XY: 15414AN XY: 135792
GnomAD4 exome AF: 0.103 AC: 150203AN: 1461864Hom.: 8478 Cov.: 32 AF XY: 0.106 AC XY: 76757AN XY: 727234
GnomAD4 genome ? AF: 0.0790 AC: 12029AN: 152274Hom.: 663 Cov.: 32 AF XY: 0.0791 AC XY: 5887AN XY: 74458
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
ZNF526-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at