chr18-14105111-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145287.4(ZNF519):c.1429C>G(p.Gln477Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000223 in 1,613,136 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.1429C>G | p.Gln477Glu | missense_variant | 3/3 | ENST00000590202.3 | |
ZNF519 | NR_033354.2 | n.162-20035C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF519 | ENST00000590202.3 | c.1429C>G | p.Gln477Glu | missense_variant | 3/3 | 1 | NM_145287.4 | P1 | |
ENST00000592926.1 | n.402G>C | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152142Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000721 AC: 18AN: 249526Hom.: 0 AF XY: 0.0000741 AC XY: 10AN XY: 134962
GnomAD4 exome AF: 0.000236 AC: 345AN: 1460994Hom.: 0 Cov.: 34 AF XY: 0.000230 AC XY: 167AN XY: 726764
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152142Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.1429C>G (p.Q477E) alteration is located in exon 3 (coding exon 3) of the ZNF519 gene. This alteration results from a C to G substitution at nucleotide position 1429, causing the glutamine (Q) at amino acid position 477 to be replaced by a glutamic acid (E). 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