chr18-14106052-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145287.4(ZNF519):c.488A>G(p.Asn163Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000283 in 1,591,838 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145287.4 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 |
---|---|---|---|---|---|---|---|
ZNF519 | NM_145287.4 | c.488A>G | p.Asn163Ser | missense_variant | 3/3 | ENST00000590202.3 | |
ZNF519 | NR_033354.2 | n.162-20976A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF519 | ENST00000590202.3 | c.488A>G | p.Asn163Ser | missense_variant | 3/3 | 1 | NM_145287.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152208Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000432 AC: 1AN: 231700Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 125900
GnomAD4 exome AF: 0.0000278 AC: 40AN: 1439630Hom.: 0 Cov.: 31 AF XY: 0.0000293 AC XY: 21AN XY: 716120
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152208Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2022 | The c.488A>G (p.N163S) alteration is located in exon 3 (coding exon 3) of the ZNF519 gene. This alteration results from a A to G substitution at nucleotide position 488, causing the asparagine (N) at amino acid position 163 to be replaced by a serine (S). 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