19-44428323-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014518.4(ZNF229):c.2458G>T(p.Gly820Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,459,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014518.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF229 | NM_014518.4 | c.2458G>T | p.Gly820Cys | missense_variant | 6/6 | ENST00000614049.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF229 | ENST00000614049.5 | c.2458G>T | p.Gly820Cys | missense_variant | 6/6 | 1 | NM_014518.4 | A2 | |
ZNF229 | ENST00000613197.4 | c.2440G>T | p.Gly814Cys | missense_variant | 6/6 | 1 | P4 | ||
ZNF229 | ENST00000620012.4 | c.*2661G>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/6 | 1 | ||||
ZNF229 | ENST00000591289.5 | n.523-10777G>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248814Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134860
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1459790Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 725846
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 12, 2021 | The c.2458G>T (p.G820C) alteration is located in exon 6 (coding exon 4) of the ZNF229 gene. This alteration results from a G to T substitution at nucleotide position 2458, causing the glycine (G) at amino acid position 820 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