chr19-21405819-G-C
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001076678.3(ZNF493):c.216G>C(p.Trp72Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000911 in 1,547,784 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_001076678.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF493 | ENST00000392288.7 | c.216G>C | p.Trp72Cys | missense_variant | Exon 3 of 4 | 1 | NM_001076678.3 | ENSP00000376110.2 | ||
ENSG00000269237 | ENST00000600810.1 | n.159G>C | non_coding_transcript_exon_variant | Exon 2 of 5 | 3 | ENSP00000473166.1 |
Frequencies
GnomAD3 genomes AF: 0.0000612 AC: 9AN: 147130Hom.: 0 Cov.: 30 show subpopulations
GnomAD2 exomes AF: 0.0000718 AC: 18AN: 250744 AF XY: 0.0000885 show subpopulations
GnomAD4 exome AF: 0.0000942 AC: 132AN: 1400654Hom.: 0 Cov.: 31 AF XY: 0.000105 AC XY: 73AN XY: 695740 show subpopulations
GnomAD4 genome AF: 0.0000612 AC: 9AN: 147130Hom.: 0 Cov.: 30 AF XY: 0.0000280 AC XY: 2AN XY: 71418 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.216G>C (p.W72C) alteration is located in exon 3 (coding exon 3) of the ZNF493 gene. This alteration results from a G to C substitution at nucleotide position 216, causing the tryptophan (W) at amino acid position 72 to be replaced by a cysteine (C). 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