19-7519569-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018083.5(ZNF358):c.327C>G(p.Asn109Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,601,650 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018083.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF358 | ENST00000597229.2 | c.327C>G | p.Asn109Lys | missense_variant | Exon 2 of 2 | 2 | NM_018083.5 | ENSP00000472305.1 | ||
ZNF358 | ENST00000596712.1 | c.327C>G | p.Asn109Lys | missense_variant | Exon 2 of 2 | 3 | ENSP00000472777.1 | |||
ENSG00000267952 | ENST00000597384.1 | n.581C>G | non_coding_transcript_exon_variant | Exon 3 of 3 | 3 | |||||
ENSG00000267952 | ENST00000599312.1 | c.*281C>G | downstream_gene_variant | 2 | ENSP00000469588.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000416 AC: 1AN: 240100Hom.: 0 AF XY: 0.00000764 AC XY: 1AN XY: 130806
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1449510Hom.: 0 Cov.: 43 AF XY: 0.00000970 AC XY: 7AN XY: 721518
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.327C>G (p.N109K) alteration is located in exon 2 (coding exon 1) of the ZNF358 gene. This alteration results from a C to G substitution at nucleotide position 327, causing the asparagine (N) at amino acid position 109 to be replaced by a lysine (K). 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