20-18315090-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001352452.2(ZNF133):āc.239A>Gā(p.Tyr80Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000712 in 1,545,388 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (ā ).
Frequency
Consequence
NM_001352452.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF133 | NM_001352452.2 | c.239A>G | p.Tyr80Cys | missense_variant | 7/7 | ENST00000425686.3 | NP_001339381.2 | |
ZNF133-AS1 | XR_937299.4 | n.574-1127T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF133 | ENST00000425686.3 | c.239A>G | p.Tyr80Cys | missense_variant | 7/7 | 3 | NM_001352452.2 | ENSP00000406638 | A2 | |
ZNF133-AS1 | ENST00000436848.1 | n.22T>C | non_coding_transcript_exon_variant | 1/2 | 2 | |||||
ENST00000666293.1 | n.425+8554T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000202 AC: 4AN: 198198Hom.: 0 AF XY: 0.0000192 AC XY: 2AN XY: 104402
GnomAD4 exome AF: 0.00000287 AC: 4AN: 1393202Hom.: 0 Cov.: 29 AF XY: 0.00000438 AC XY: 3AN XY: 685072
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 18, 2024 | The c.236A>G (p.Y79C) alteration is located in exon 7 (coding exon 3) of the ZNF133 gene. This alteration results from a A to G substitution at nucleotide position 236, causing the tyrosine (Y) at amino acid position 79 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at