chr19-12015545-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001308348.2(ZNF433):c.1313G>T(p.Gly438Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001308348.2 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 | UniProt |
---|---|---|---|---|---|---|---|
ZNF433 | NM_001308348.2 | c.1313G>T | p.Gly438Val | missense_variant | 4/4 | ENST00000550507.7 | |
ZNF433-AS1 | NR_134928.1 | n.256+13723C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF433 | ENST00000550507.7 | c.1313G>T | p.Gly438Val | missense_variant | 4/4 | 2 | NM_001308348.2 | A2 | |
ZNF433-AS1 | ENST00000476474.5 | n.194+13723C>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000265 AC: 4AN: 151154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250916Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135784
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461846Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727218
GnomAD4 genome ? AF: 0.0000265 AC: 4AN: 151154Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 73768
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.1322G>T (p.G441V) alteration is located in exon 4 (coding exon 4) of the ZNF433 gene. This alteration results from a G to T substitution at nucleotide position 1322, causing the glycine (G) at amino acid position 441 to be replaced by a valine (V). 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