chr19-22391757-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001098626.2(ZNF98):c.1478A>G(p.Glu493Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000263 in 1,602,474 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001098626.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF98 | NM_001098626.2 | c.1478A>G | p.Glu493Gly | missense_variant | 4/4 | ENST00000357774.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF98 | ENST00000357774.9 | c.1478A>G | p.Glu493Gly | missense_variant | 4/4 | 1 | NM_001098626.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000526 AC: 80AN: 152128Hom.: 2 Cov.: 32
GnomAD4 exome AF: 0.000235 AC: 341AN: 1450346Hom.: 3 Cov.: 33 AF XY: 0.000234 AC XY: 169AN XY: 721276
GnomAD4 genome ? AF: 0.000526 AC: 80AN: 152128Hom.: 2 Cov.: 32 AF XY: 0.000511 AC XY: 38AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.1478A>G (p.E493G) alteration is located in exon 4 (coding exon 4) of the ZNF98 gene. This alteration results from a A to G substitution at nucleotide position 1478, causing the glutamic acid (E) at amino acid position 493 to be replaced by a glycine (G). 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