chr19-42224917-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_133444.3(ZNF526):c.514C>A(p.Pro172Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000104 in 1,614,188 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_133444.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF526 | NM_133444.3 | c.514C>A | p.Pro172Thr | missense_variant | 3/3 | ENST00000301215.8 | |
ZNF526 | NM_001314033.3 | c.514C>A | p.Pro172Thr | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF526 | ENST00000301215.8 | c.514C>A | p.Pro172Thr | missense_variant | 3/3 | 1 | NM_133444.3 | P1 | |
ZNF526 | ENST00000710326.1 | c.514C>A | p.Pro172Thr | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000115 AC: 29AN: 251280Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135826
GnomAD4 exome AF: 0.000107 AC: 156AN: 1461888Hom.: 2 Cov.: 32 AF XY: 0.000114 AC XY: 83AN XY: 727246
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74478
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 16, 2022 | The c.514C>A (p.P172T) alteration is located in exon 3 (coding exon 1) of the ZNF526 gene. This alteration results from a C to A substitution at nucleotide position 514, causing the proline (P) at amino acid position 172 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 02, 2022 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at