chr19-42224969-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_133444.3(ZNF526):c.566C>T(p.Pro189Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0117 in 1,614,236 control chromosomes in the GnomAD database, including 139 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_133444.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF526 | NM_133444.3 | c.566C>T | p.Pro189Leu | missense_variant | 3/3 | ENST00000301215.8 | |
ZNF526 | NM_001314033.3 | c.566C>T | p.Pro189Leu | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF526 | ENST00000301215.8 | c.566C>T | p.Pro189Leu | missense_variant | 3/3 | 1 | NM_133444.3 | P1 | |
ZNF526 | ENST00000710326.1 | c.566C>T | p.Pro189Leu | missense_variant | 3/3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00738 AC: 1123AN: 152224Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00780 AC: 1961AN: 251404Hom.: 11 AF XY: 0.00785 AC XY: 1066AN XY: 135876
GnomAD4 exome AF: 0.0121 AC: 17714AN: 1461894Hom.: 134 Cov.: 32 AF XY: 0.0118 AC XY: 8564AN XY: 727248
GnomAD4 genome AF: 0.00737 AC: 1123AN: 152342Hom.: 5 Cov.: 32 AF XY: 0.00677 AC XY: 504AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 18, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at