chr19-22391887-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001098626.2(ZNF98):c.1348A>G(p.Thr450Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000299 in 1,312,762 control chromosomes in the GnomAD database, including 92 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF98 | NM_001098626.2 | c.1348A>G | p.Thr450Ala | missense_variant | 4/4 | ENST00000357774.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF98 | ENST00000357774.9 | c.1348A>G | p.Thr450Ala | missense_variant | 4/4 | 1 | NM_001098626.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000896 AC: 11AN: 122824Hom.: 0 Cov.: 25
GnomAD3 exomes AF: 0.0000778 AC: 15AN: 192868Hom.: 1 AF XY: 0.0000775 AC XY: 8AN XY: 103246
GnomAD4 exome AF: 0.000321 AC: 382AN: 1189938Hom.: 92 Cov.: 32 AF XY: 0.000316 AC XY: 187AN XY: 592656
GnomAD4 genome ? AF: 0.0000896 AC: 11AN: 122824Hom.: 0 Cov.: 25 AF XY: 0.0000508 AC XY: 3AN XY: 59040
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 06, 2023 | The c.1348A>G (p.T450A) 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 1348, causing the threonine (T) at amino acid position 450 to be replaced by an alanine (A). 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