chr18-14105126-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145287.4(ZNF519):c.1414G>A(p.Gly472Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000993 in 1,611,356 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.1414G>A | p.Gly472Ser | missense_variant | 3/3 | ENST00000590202.3 | |
ZNF519 | NR_033354.2 | n.162-20050G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF519 | ENST00000590202.3 | c.1414G>A | p.Gly472Ser | missense_variant | 3/3 | 1 | NM_145287.4 | P1 | |
ENST00000592926.1 | n.417C>T | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000733 AC: 11AN: 150006Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249850Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135192
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461218Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 726862
GnomAD4 genome ? AF: 0.0000733 AC: 11AN: 150138Hom.: 0 Cov.: 33 AF XY: 0.000109 AC XY: 8AN XY: 73286
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2022 | The c.1414G>A (p.G472S) alteration is located in exon 3 (coding exon 3) of the ZNF519 gene. This alteration results from a G to A substitution at nucleotide position 1414, causing the glycine (G) at amino acid position 472 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