rs200018551
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_133444.3(ZNF526):c.1675G>A(p.Ala559Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000192 in 1,606,912 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_133444.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF526 | NM_133444.3 | c.1675G>A | p.Ala559Thr | missense_variant | 3/3 | ENST00000301215.8 | |
ZNF526 | NM_001314033.3 | c.1675G>A | p.Ala559Thr | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF526 | ENST00000301215.8 | c.1675G>A | p.Ala559Thr | missense_variant | 3/3 | 1 | NM_133444.3 | P1 | |
ZNF526 | ENST00000710326.1 | c.1675G>A | p.Ala559Thr | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00102 AC: 250AN: 243948Hom.: 0 AF XY: 0.000596 AC XY: 79AN XY: 132658
GnomAD4 exome AF: 0.000201 AC: 292AN: 1454616Hom.: 0 Cov.: 35 AF XY: 0.000146 AC XY: 106AN XY: 723938
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152296Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74448
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 23, 2017 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 12, 2018 | - - |
ZNF526-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 21, 2020 | This variant is classified as likely 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