chr19-21423177-A-G
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001076678.3(ZNF493):c.518A>G(p.Asn173Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,646 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001076678.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF493 | ENST00000392288.7 | c.518A>G | p.Asn173Ser | missense_variant | Exon 4 of 4 | 1 | NM_001076678.3 | ENSP00000376110.2 | ||
ENSG00000269237 | ENST00000600810.1 | n.196+17321A>G | intron_variant | Intron 2 of 4 | 3 | ENSP00000473166.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000240 AC: 6AN: 250046 AF XY: 0.0000295 show subpopulations
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461420Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727004 show subpopulations
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74356 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.518A>G (p.N173S) alteration is located in exon 4 (coding exon 4) of the ZNF493 gene. This alteration results from a A to G substitution at nucleotide position 518, causing the asparagine (N) at amino acid position 173 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