19-22391586-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001098626.2(ZNF98):c.1649G>A(p.Ser550Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000454 in 1,454,202 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF98 | NM_001098626.2 | c.1649G>A | p.Ser550Asn | missense_variant | 4/4 | ENST00000357774.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF98 | ENST00000357774.9 | c.1649G>A | p.Ser550Asn | missense_variant | 4/4 | 1 | NM_001098626.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152108Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000454 AC: 66AN: 1454202Hom.: 0 Cov.: 32 AF XY: 0.0000484 AC XY: 35AN XY: 722896
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000263 AC: 4AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.1649G>A (p.S550N) alteration is located in exon 4 (coding exon 4) of the ZNF98 gene. This alteration results from a G to A substitution at nucleotide position 1649, causing the serine (S) at amino acid position 550 to be replaced by an asparagine (N). 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