chr18-14106063-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_145287.4(ZNF519):c.477G>T(p.Gln159His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00167 in 1,595,634 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF519 | NM_145287.4 | c.477G>T | p.Gln159His | missense_variant | 3/3 | ENST00000590202.3 | |
ZNF519 | NR_033354.2 | n.162-20987G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF519 | ENST00000590202.3 | c.477G>T | p.Gln159His | missense_variant | 3/3 | 1 | NM_145287.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00100 AC: 152AN: 152068Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000813 AC: 190AN: 233574Hom.: 0 AF XY: 0.000827 AC XY: 105AN XY: 126900
GnomAD4 exome AF: 0.00174 AC: 2513AN: 1443448Hom.: 2 Cov.: 31 AF XY: 0.00173 AC XY: 1242AN XY: 717818
GnomAD4 genome ? AF: 0.000999 AC: 152AN: 152186Hom.: 0 Cov.: 31 AF XY: 0.000874 AC XY: 65AN XY: 74400
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2022 | The c.477G>T (p.Q159H) alteration is located in exon 3 (coding exon 3) of the ZNF519 gene. This alteration results from a G to T substitution at nucleotide position 477, causing the glutamine (Q) at amino acid position 159 to be replaced by a histidine (H). 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